Contacts of the helix formed by residues 3 - 20 (chain B) in PDB entry 4EVI
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 ALA 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 4.6 7.4 - - - +
192A SER* 3.6 33.4 - - - +
1B MET 3.9 0.4 + - - -
2B ASP* 1.3 73.8 - - - +
4B ALA* 1.3 62.4 + - - +
6B ALA* 3.2 8.3 + - - +
7B VAL* 2.9 31.1 + - + +
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 3.3 14.6 + - - +
3B ALA* 1.3 79.0 - - - +
5B THR* 1.3 62.0 + - - +
7B VAL* 3.5 6.9 + - - +
8B GLU* 3.1 23.8 + - - +
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Residues in contact with THR 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.5 12.3 - - - +
1B MET* 3.7 29.6 - - + -
2B ASP* 2.7 26.0 + - - -
4B ALA* 1.3 74.2 - - - +
6B ALA* 1.3 59.2 + - - +
8B GLU* 3.3 9.1 + - + +
9B LEU* 3.0 38.2 + - + +
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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
----------------------------------------------------------
185A LEU* 3.9 16.0 - - + +
188A ARG* 3.7 32.1 - - + -
189A ALA* 4.5 2.7 - - - +
1B MET* 3.5 18.0 - - - -
2B ASP 3.1 11.9 + - - +
3B ALA* 3.2 9.8 + - - +
5B THR* 1.3 78.3 - - - +
7B VAL* 1.3 55.9 + - - +
9B LEU* 3.4 1.7 + - - +
10B LEU* 2.8 30.5 + - - +
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA* 3.8 24.7 - - + -
192A SER* 5.6 1.6 - - - +
193A LYS* 4.2 33.2 - - + +
357A VAL 4.3 6.1 - - - +
3B ALA* 2.9 26.2 + - + +
4B ALA* 3.8 6.5 - - - +
6B ALA* 1.3 71.9 - - - +
8B GLU* 1.3 61.5 + - - +
10B LEU* 3.2 7.6 + - + +
11B ASP* 2.9 45.3 + - - +
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 2.9 37.4 + - - +
4B ALA 3.1 17.5 + - - +
5B THR* 3.3 9.0 + - - +
7B VAL* 1.3 77.2 - - - +
9B LEU* 1.3 61.2 + - - +
11B ASP* 3.3 7.0 + - - +
12B ALA* 3.1 21.7 + - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO 5.2 0.4 - - - +
105A ARG* 3.5 50.9 - - + +
106A LEU* 4.2 14.8 - - + +
113A TYR* 3.6 22.2 - - + +
185A LEU* 3.6 20.3 - - + +
1B MET* 3.5 33.4 - - + -
5B THR* 3.0 24.3 + - + +
8B GLU* 1.3 72.9 - - + +
10B LEU* 1.3 66.8 + - - +
12B ALA* 3.0 16.2 + - + +
13B GLN* 3.2 16.3 + - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 3.9 7.9 - - + +
186A PHE* 3.8 29.8 - - + +
189A ALA* 3.5 28.0 - - + -
357A VAL 4.1 0.9 - - - +
358A GLY* 3.6 29.2 - - - +
359A GLY* 3.5 11.3 - - - +
361A ARG* 3.7 19.3 - - - +
6B ALA 2.8 22.9 + - - +
7B VAL* 3.2 6.3 + - - +
9B LEU* 1.3 74.2 - - - +
11B ASP* 1.3 60.5 + - - +
12B ALA 3.3 0.2 + - - -
13B GLN* 3.4 30.7 + - - +
14B PRO* 3.4 14.9 - - - +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 5.3 1.7 + - - -
357A VAL 5.0 0.2 - - - +
358A GLY* 3.2 11.5 - - - -
359A GLY* 2.8 31.8 + - - +
7B VAL* 2.9 33.1 + - - +
8B GLU* 3.8 6.4 - - - +
9B LEU 3.2 0.2 - - - -
10B LEU* 1.3 76.3 - - - +
12B ALA* 1.3 58.0 + - - +
13B GLN 3.4 0.2 - - - -
14B PRO* 3.3 14.0 - - - +
15B GLN* 4.4 6.9 + - - +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.9 24.4 - - + +
105A ARG* 5.5 5.2 - - - +
106A LEU* 3.9 7.9 - - + -
8B GLU* 3.1 12.3 + - + +
9B LEU* 3.0 16.9 + - + +
11B ASP* 1.3 76.7 - - - +
13B GLN* 1.3 66.8 + - - +
14B PRO 3.3 1.1 - - - -
15B GLN* 3.2 33.1 + - - +
16B VAL* 3.7 2.3 + - - +
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.7 19.9 - - + +
113A TYR 4.5 5.0 - - - +
115A ALA* 5.3 8.6 - - + +
118A LEU* 6.0 0.5 - - - +
181A GLY 4.4 1.6 - - - +
182A ASP* 2.9 45.8 + - - +
185A LEU* 3.8 17.5 - - + +
361A ARG* 4.2 0.4 - - - +
9B LEU 3.2 12.3 + - - +
10B LEU* 3.5 25.4 + - - +
12B ALA* 1.3 78.2 - - - +
14B PRO* 1.3 70.1 - - + +
16B VAL* 2.8 16.3 + - - +
17B TRP* 2.9 34.8 + - + +
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Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A SER* 6.2 0.4 - - - -
318A THR* 3.6 10.9 + - + +
359A GLY* 3.8 15.3 - - - -
360A LEU* 3.8 37.9 - - + -
10B LEU 3.4 10.5 - - - +
11B ASP 3.3 18.4 - - - +
12B ALA 3.4 0.4 - - - -
13B GLN* 1.3 90.7 - - + +
15B GLN* 1.3 55.3 + - + +
17B TRP* 3.7 20.0 - - + -
18B HIS* 2.8 31.0 + - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.9 27.4 - - + +
11B ASP 4.4 5.0 + - - +
12B ALA* 3.4 28.7 - - - +
13B GLN 3.1 0.8 - - - -
14B PRO* 1.3 77.2 - - - +
16B VAL* 1.3 63.5 + - - +
18B HIS* 3.5 6.5 + - - +
19B HIS* 3.2 33.2 + - + -
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Residues in contact with VAL 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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29A LEU* 3.9 7.6 - - + -
79A TYR* 3.4 32.3 - - + +
103A LEU* 4.0 16.8 - - + -
106A LEU* 3.8 31.9 - - + -
107A LEU* 4.8 6.1 - - + -
115A ALA* 4.6 15.0 - - + -
119A THR* 4.7 2.0 - - - +
12B ALA 4.0 0.4 - - - +
13B GLN* 2.8 9.0 + - - +
15B GLN* 1.3 74.4 - - - +
17B TRP* 1.3 66.8 + - + +
19B HIS* 3.0 4.5 + - - +
20B PHE* 2.9 40.8 + - + -
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Residues in contact with TRP 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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115A ALA* 5.4 5.2 - - + +
118A LEU* 3.6 17.4 - - + +
182A ASP* 3.7 13.2 - - + -
268A TRP* 3.7 27.4 - + - -
303A HIS* 4.9 0.2 - + - -
318A THR* 4.4 6.3 - - + -
322A LEU* 4.0 29.6 - - + -
359A GLY 3.9 13.9 - - - -
360A LEU* 4.1 4.5 - - + -
361A ARG* 3.5 22.7 - - - -
402A C9M 4.7 4.9 - + - -
13B GLN* 2.9 38.0 + - + +
14B PRO* 3.6 26.9 - - + +
16B VAL* 1.3 77.8 - - + +
18B HIS* 1.3 57.4 + - - +
20B PHE* 3.5 31.2 - + + -
21B LEU* 2.9 44.9 + - + +
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASN* 4.3 7.7 + - + +
317A GLY* 4.2 1.3 - - - -
318A THR* 2.7 36.1 + - - +
321A ILE* 3.8 17.8 - - + +
14B PRO 2.8 17.9 + - - +
15B GLN* 3.6 8.5 - - - +
16B VAL 3.1 0.2 - - - -
17B TRP* 1.3 76.1 - - - +
19B HIS* 1.3 66.0 + + + +
21B LEU* 3.6 4.0 + - - -
22B GLY* 3.3 11.4 + - - -
402B GOL 3.2 44.8 + - - -
404B GOL 2.9 30.4 + - - -
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.4 33.3 - - + +
26A SER 3.4 3.3 + - - -
29A LEU* 4.0 8.1 - - + -
77A LEU* 3.2 54.1 + - + +
79A TYR* 2.7 34.7 + + + +
103A LEU* 4.5 6.3 - - + -
15B GLN* 3.2 15.0 + - + -
16B VAL 3.0 7.1 + - - +
18B HIS* 1.3 83.1 - + + +
20B PHE* 1.3 61.6 + - - +
22B GLY 3.1 10.2 + - - -
404B GOL 3.7 4.7 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 2.7 29.1 + - - +
29A LEU* 4.1 7.9 - - + -
115A ALA* 4.7 3.6 - - + -
118A LEU* 3.9 13.7 - - + -
119A THR* 3.2 47.8 - - + -
122A SER* 3.2 33.4 - - - -
123A VAL* 3.4 16.0 - - + +
402A C9M 3.3 14.1 - - - -
16B VAL* 2.9 34.9 + - + -
17B TRP* 3.5 36.3 - + - -
19B HIS* 1.3 74.4 - - - +
21B LEU* 1.3 66.7 + - + +
22B GLY 3.2 1.1 - - - -
23B TYR* 3.5 5.0 - - - -
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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
------------------------------------------------------------
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