Contacts of the helix formed by residues 2 - 22 (chain B) in PDB entry 1UHG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GLY* 1.3 81.1 + - - +
3B ILE* 1.3 61.1 + - - +
4B GLY* 3.7 4.0 + - - -
5B ALA* 3.2 23.4 + - - +
6B ALA* 2.9 29.8 + - - +
62B LEU* 3.4 7.8 - - - +
63B PRO* 5.0 2.9 - - - -
373B THR 5.7 1.3 - - - -
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Residues in contact with ILE 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 1.3 72.2 - - - +
4B GLY* 1.3 61.2 + - - +
6B ALA* 4.4 0.7 - - - -
7B SER* 2.7 39.9 + - - +
32B ILE* 4.4 5.8 - - + -
35B MET* 3.9 26.9 - - + -
62B LEU* 3.7 19.0 - - + +
82B SER* 4.0 24.6 - - - +
83B LEU* 3.9 21.3 - - + -
86B ILE* 3.8 33.7 - - + -
373B THR* 4.0 16.8 - - + +
375B ALA* 4.3 4.9 - - + -
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Residues in contact with GLY 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.1 5.0 + - - -
3B ILE* 1.3 83.8 - - - +
5B ALA* 1.3 57.9 + - - +
7B SER* 3.2 2.3 + - - -
8B MET* 2.9 36.5 + - - +
261B PHE* 4.7 2.9 - - - -
373B THR 3.4 22.5 + - - -
374B ASN* 4.0 4.9 - - - -
375B ALA* 3.9 12.8 - - - -
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLY 4.7 6.5 - - - +
2B SER* 3.2 25.1 + - - +
4B GLY* 1.3 75.0 - - - +
6B ALA* 1.3 58.0 + - - +
8B MET* 3.8 1.0 - - - +
9B GLU* 2.9 31.5 + - - +
61B LYS* 6.2 0.2 - - - -
261B PHE* 3.4 38.7 - - + -
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Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER 2.9 16.7 + - - +
3B ILE* 4.0 2.7 - - - +
5B ALA* 1.3 74.9 - - - +
7B SER* 1.3 60.1 + - - +
9B GLU* 4.0 4.0 - - - +
10B PHE* 2.9 30.3 + - - +
35B MET* 4.3 8.1 - - + +
57B VAL 4.5 2.3 - - - +
58B ARG* 4.2 20.2 + - + +
61B LYS* 4.2 10.7 - - - +
62B LEU* 4.0 26.7 - - + -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 2.7 27.6 + - - -
4B GLY 3.2 3.6 + - - -
6B ALA* 1.3 72.5 - - - +
8B MET* 1.3 60.7 + - - +
10B PHE* 3.8 1.0 - - - +
11B CYS* 2.8 31.8 + - - +
31B PRO* 4.5 3.2 - - - +
32B ILE* 4.2 15.5 - - - -
35B MET* 3.6 26.3 - - - +
375B ALA* 3.3 4.7 - - - -
376B VAL* 3.1 30.2 + - - -
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLY 2.9 20.5 + - - +
7B SER* 1.3 79.4 + - - +
9B GLU* 1.3 62.7 + - - +
11B CYS* 3.4 1.8 + - - +
12B PHE* 3.0 38.3 + - + -
261B PHE* 3.5 30.1 - - + -
264B LEU* 3.6 35.0 - - + -
265B THR* 3.5 26.7 - - + +
268B THR* 6.1 0.4 - - - +
369B LYS* 6.0 4.5 - - + +
374B ASN* 3.9 25.4 - - + +
376B VAL* 3.2 26.7 - - + -
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA 2.9 18.8 + - - +
6B ALA* 4.1 3.6 - - - +
7B SER 3.3 0.2 - - - -
8B MET* 1.3 74.6 - - - +
10B PHE* 1.3 66.8 + - - +
12B PHE* 3.3 5.1 + - + +
13B ASP* 3.0 32.0 + - - +
58B ARG* 2.5 42.3 + - + +
261B PHE* 4.4 18.2 - - + +
262B GLU* 4.4 14.0 - - - +
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA 2.9 19.7 + - - +
7B SER 3.8 2.5 - - - +
9B GLU* 1.3 75.7 - - - +
11B CYS* 1.3 65.2 + - - +
13B ASP* 3.0 8.8 + - - +
14B VAL* 2.9 42.4 + - + +
31B PRO* 4.1 10.8 - - + -
34B ILE* 3.7 35.9 - - + -
35B MET* 3.4 33.2 - - + -
38B LEU* 4.2 9.4 - - + -
56B VAL* 3.6 22.9 - - + -
57B VAL* 4.1 23.6 - - + +
58B ARG* 3.9 3.3 - - - +
297B LEU* 4.4 6.5 - - + -
300B MET* 3.6 22.2 - - + -
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Residues in contact with CYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER 2.8 19.7 + - - +
8B MET* 3.4 8.7 - - - +
10B PHE* 1.3 78.1 - - - +
12B PHE* 1.3 64.1 + - - +
14B VAL* 3.3 1.9 + - - +
15B PHE 2.9 12.5 + - - -
29B TYR* 2.7 28.8 + - - -
31B PRO* 3.7 26.5 - - + -
376B VAL* 4.1 10.1 - - + -
379B PHE* 3.5 42.4 - - - -
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 3.0 40.0 + - + +
9B GLU* 3.3 4.0 + - + +
11B CYS* 1.3 79.6 - - - +
13B ASP* 1.3 63.5 + - - +
15B PHE* 4.0 8.1 - + + -
16B LYS* 2.8 41.6 + - + +
259B ILE* 3.7 42.4 - - + +
260B ASN* 3.7 24.7 - - + -
261B PHE* 3.4 20.6 - - + +
264B LEU* 4.1 15.5 - - + -
376B VAL* 5.6 1.6 - - + -
379B PHE* 3.7 35.2 - + - -
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Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 3.0 14.0 + - - +
10B PHE* 3.0 7.8 + - - +
12B PHE* 1.3 78.1 - - - +
14B VAL* 1.3 62.5 + - - +
16B LYS* 3.4 9.6 + - - +
17B GLU* 3.2 20.4 + - - +
56B VAL 4.7 2.0 - - - +
58B ARG* 2.8 42.6 + - - -
300B MET* 3.8 22.9 - - + +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 2.9 47.7 + - + +
11B CYS* 3.5 8.1 - - - +
13B ASP* 1.3 77.4 - - - +
15B PHE* 1.3 63.3 + - - +
17B GLU* 3.0 5.4 + - - +
18B LEU* 2.9 35.4 + - + +
29B TYR* 3.5 30.1 - - + -
34B ILE* 5.1 8.3 - - + -
293B LEU* 6.5 0.7 - - + -
296B VAL* 4.5 10.5 - - + -
297B LEU* 5.6 1.1 - - + -
300B MET* 3.8 17.7 - - + -
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Residues in contact with PHE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B CYS 2.9 11.3 + - - +
12B PHE* 3.3 9.8 + + - +
14B VAL* 1.3 76.7 - - - +
16B LYS* 1.3 74.9 + - + +
18B LEU* 3.3 3.7 + - + +
19B LYS* 3.0 52.6 + - + +
27B ILE* 3.8 29.2 - - + -
29B TYR* 3.3 22.0 + + - +
256B GLU* 3.8 38.8 - - + -
259B ILE* 4.7 7.0 - - + -
365B LEU* 4.1 7.0 - - + -
379B PHE* 3.5 37.5 - + + -
381B ARG* 4.5 7.2 - - + -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 2.8 36.4 + - + +
13B ASP* 3.6 9.6 - - - +
14B VAL 3.2 0.2 - - - -
15B PHE* 1.3 90.1 - - + +
17B GLU* 1.3 61.5 + - - +
19B LYS* 3.4 31.0 + - - +
20B VAL* 3.6 15.8 - - - +
256B GLU 2.9 27.7 + - - -
257B SER* 4.5 7.9 + - - +
259B ILE* 3.8 20.0 - - - -
260B ASN* 6.0 0.4 - - - -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP 3.2 9.4 + - - +
14B VAL 3.0 8.5 + - - +
16B LYS* 1.3 77.8 - - - +
18B LEU* 1.3 66.2 + - - +
20B VAL* 3.2 27.5 + - - +
21B HIS* 3.9 24.4 + - + -
295B SER 5.2 0.2 - - - +
296B VAL* 3.7 25.1 - - + +
299B ALA* 3.2 41.4 - - + +
300B MET* 4.3 10.6 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 2.9 26.5 + - + +
15B PHE* 3.9 4.7 - - - +
17B GLU* 1.3 75.7 - - - +
19B LYS* 1.3 63.8 + - - +
20B VAL 3.2 0.3 + - - -
21B HIS* 3.2 2.6 + - - +
22B HIS* 3.1 37.9 + - + +
27B ILE* 3.7 19.1 - - + -
29B TYR* 3.6 37.9 - - + -
291B TYR* 3.7 34.1 - - + -
296B VAL* 3.6 31.0 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.0 48.2 + - + +
16B LYS* 3.4 41.1 - - - +
17B GLU 3.2 0.4 - - - -
18B LEU* 1.3 76.3 - - - +
20B VAL* 1.3 64.9 + - + +
21B HIS 3.3 0.7 + - - -
22B HIS 3.5 7.1 + - - +
23B ALA* 3.9 13.3 + - - +
27B ILE* 4.6 2.9 - - - +
253B GLU* 5.2 4.0 + - - -
256B GLU* 3.2 38.1 + - + +
257B SER* 4.5 8.3 + - - +
381B ARG* 4.0 12.0 + - - +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 3.6 17.0 - - - +
17B GLU* 3.5 18.8 - - - +
18B LEU 3.2 0.8 - - - -
19B LYS* 1.3 80.0 - - + +
21B HIS* 1.3 80.0 + - + +
23B ALA* 5.0 1.4 + - - +
61D LYS* 4.4 15.1 + - - -
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Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.9 25.5 + - + +
18B LEU 3.2 3.6 + - - +
20B VAL* 1.3 93.6 + - + +
22B HIS* 1.3 79.8 + - + +
23B ALA 3.8 1.8 - - - -
25B GLU* 4.2 2.1 - - - +
66D GLY* 4.5 16.5 - - - -
67D ASP* 5.3 4.9 + - + +
68D SEP 3.5 46.1 + - - +
69D ILE* 5.3 0.7 + - - +
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Residues in contact with HIS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.1 35.0 + - + +
19B LYS* 3.5 5.1 + - - -
21B HIS* 1.3 91.0 + - + +
23B ALA* 1.3 64.0 + - - +
25B GLU* 3.1 31.8 + - + +
26B ASN 5.3 1.8 + - - +
27B ILE* 4.4 14.8 - - + -
290B LYS 5.5 1.6 - - - -
291B TYR* 3.7 36.2 - + - -
381B ARG* 2.9 22.2 + - - -
68D SEP 4.5 14.7 + - - -
69D ILE* 4.5 29.2 - - + +
72D GLN* 6.3 1.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il