Contacts of the helix formed by residues 52 - 68 (chain B) in PDB entry 1H3F
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 HIS 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A SO4 2.8 32.0 + - - -
50B ASP 4.8 2.7 - - - -
51B LEU* 1.3 75.4 - - - +
53B LEU* 1.3 67.9 + - - +
54B GLY* 2.9 34.3 + - - -
55B HIS* 2.9 44.0 + + - +
56B ALA 3.5 2.6 + - - -
233B MET* 3.5 25.6 - - + -
234B SER* 3.6 4.6 - - - -
235B LYS* 4.2 6.1 - - + -
240B TYR* 3.9 27.1 - + + -
241B ILE 3.1 22.4 - - - +
242B GLY* 3.9 2.5 - - - -
243B LEU* 3.6 10.5 - - - +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 1.3 71.6 - - - +
54B GLY* 1.3 62.3 + - - +
56B ALA* 3.1 17.3 + - + +
57B VAL* 3.7 3.5 + - - +
224B LEU* 3.8 15.4 - - + +
233B MET* 4.0 5.4 - - + -
241B ILE* 2.9 39.5 + - + +
243B LEU* 3.8 19.0 - - + +
250B MET* 5.0 5.6 - - + -
254B LEU* 3.8 30.3 - - + -
265B TYR* 4.7 4.3 - - + -
269B LEU* 3.7 32.2 - - + +
296B LEU* 4.2 5.8 - - + -
300B TYR* 4.0 24.2 - - + -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 2.9 22.6 + - - -
53B LEU* 1.3 80.3 - - - +
55B HIS* 1.3 60.7 + - - +
57B VAL* 3.5 17.7 + - - +
58B VAL* 4.6 1.2 + - - +
224B LEU* 4.0 22.6 + - - +
233B MET* 3.6 7.0 - - - -
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A SO4 3.7 19.0 + - - -
48B ARG* 4.9 6.5 + - - +
50B ASP 3.7 16.8 + - - -
51B LEU* 3.5 21.4 - - + +
52B HIS* 2.9 56.3 + + - +
54B GLY* 1.3 74.7 - - - +
56B ALA* 1.3 65.6 + - - +
57B VAL 3.2 0.7 + - - -
58B VAL* 3.5 6.1 + - - +
59B LEU* 3.1 39.6 + - + +
108B TYR* 5.3 6.3 - + - -
243B LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS 3.5 2.9 + - - +
53B LEU* 3.1 21.4 + - + +
55B HIS* 1.3 76.7 - - - +
57B VAL* 1.3 61.4 + - - +
59B LEU* 3.8 0.7 - - - -
60B ARG* 2.8 34.3 + - + +
115B ILE* 3.8 19.7 - - + +
243B LEU* 4.5 1.8 - - + +
268B LEU 4.9 0.7 - - - +
269B LEU* 4.3 11.2 - - + -
300B TYR* 3.5 26.9 - - + +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 4.0 7.2 - - - +
54B GLY 3.7 15.3 - - - +
55B HIS 3.2 0.6 - - - -
56B ALA* 1.3 80.7 - - - +
58B VAL* 1.3 63.1 + - + +
60B ARG* 4.4 1.0 - - - +
61B LYS* 3.6 17.2 + - - +
221B MET* 3.7 38.0 - - + +
222B PRO 3.7 14.1 - - - +
224B LEU* 4.2 17.5 - - + +
268B LEU* 4.0 44.1 - - + +
269B LEU* 4.2 5.1 - - + +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.2 16.2 - - + -
54B GLY 4.6 0.6 + - - +
55B HIS* 3.5 6.7 + - - +
57B VAL* 1.3 78.9 - - + +
59B LEU* 1.3 66.8 + - + +
61B LYS* 3.3 4.4 + - - +
62B MET* 3.2 30.4 + - - +
192B MET* 3.8 27.3 - - + +
193B GLY* 4.0 20.4 - - - +
194B GLY* 4.6 3.6 - - - +
221B MET* 3.8 30.7 - - + -
222B PRO 5.8 0.2 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 30.1 - - + -
51B LEU* 4.0 27.6 - - + -
55B HIS* 3.1 30.2 + - + +
58B VAL* 1.3 77.9 - - + +
60B ARG* 1.3 57.3 + - - +
62B MET* 3.2 9.5 + - - +
63B ARG 3.0 20.6 + - - -
74B LEU* 5.5 0.2 - - + -
108B TYR* 4.0 10.3 - - - +
112B ALA* 4.6 9.0 - - + -
115B ILE* 3.6 32.2 - - + +
116B LEU* 3.4 30.9 - - + +
243B LEU* 5.2 0.2 - - + -
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 2.8 23.6 + - - +
57B VAL* 4.4 2.2 - - - +
59B LEU* 1.3 70.9 - - - +
61B LYS* 1.3 64.0 + - - +
63B ARG* 3.2 8.4 + - + +
64B GLN* 3.1 34.5 + - - +
115B ILE* 3.7 7.4 - - + +
267B ARG 5.1 0.8 + - - -
268B LEU 4.6 6.0 + - - +
269B LEU* 3.4 20.3 + - - +
270B THR* 3.2 28.3 + - - +
271B ASP* 2.8 41.1 + - - -
300B TYR* 4.2 10.1 - - - -
305B ILE* 3.7 30.7 - - + +
306B PRO 5.6 0.4 + - - -
307B PRO 4.5 8.3 + - - +
309B ILE* 3.9 21.9 - - - +
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.6 8.1 + - - -
15B LEU* 3.0 32.9 + - + +
17B ARG* 2.8 28.8 + - - +
19B ALA 5.3 0.2 - - - +
57B VAL 3.6 11.3 + - - +
58B VAL 3.3 8.9 + - - +
59B LEU 3.3 0.2 - - - -
60B ARG* 1.3 79.6 - - - +
62B MET* 1.3 64.0 + - - +
64B GLN* 2.9 42.7 + - - +
65B PHE* 3.2 16.2 + - + -
192B MET* 3.6 23.6 - - + -
219B PHE* 3.8 14.8 - - + -
221B MET* 4.1 18.6 - - - -
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.3 8.5 - - + +
42B LEU* 3.5 48.0 - - + +
58B VAL* 3.2 23.4 + - - +
59B LEU* 3.3 11.9 - - - +
61B LYS* 1.3 75.7 - - - +
63B ARG* 1.3 65.0 + - - +
65B PHE* 3.0 12.9 + - - +
66B GLN* 3.0 24.1 + - - +
72B VAL* 3.3 37.3 - - + +
74B LEU* 5.2 1.1 - - + -
116B LEU* 3.7 17.7 - - + -
192B MET* 3.7 21.5 - - + -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU 3.0 12.0 + - - +
60B ARG* 3.2 16.1 + - + +
62B MET* 1.3 75.5 - - - +
64B GLN* 1.3 58.7 + - + +
66B GLN* 3.1 23.0 + - - +
67B GLU* 2.7 57.4 + - + +
115B ILE* 2.9 33.5 + - + +
116B LEU* 4.0 0.6 - - - +
117B ARG* 3.6 15.7 - - - +
304B GLN* 4.1 15.1 + - - +
305B ILE* 3.1 40.8 + - + +
306B PRO 4.0 1.0 + - - +
307B PRO* 3.7 30.7 - - + +
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Residues in contact with GLN 64 (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 LEU* 3.5 28.9 - - - +
15B LEU* 4.2 9.8 + - + +
17B ARG* 6.0 0.4 - - - +
60B ARG* 3.1 22.3 + - - +
61B LYS* 2.9 46.6 + - - +
63B ARG* 1.3 78.6 - - + +
65B PHE* 1.3 62.3 + - - +
67B GLU* 3.2 8.6 + - - +
68B LEU* 3.1 30.2 + - + +
271B ASP* 4.4 17.1 + - - +
307B PRO 5.1 10.3 - - - +
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Residues in contact with PHE 65 (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 LEU* 3.6 39.2 - - + +
28B LEU* 4.6 13.5 - - + -
32B LEU* 5.2 0.7 - - + -
38B LEU* 5.0 4.5 - - + -
40B VAL* 3.8 36.1 - - + -
61B LYS* 3.2 21.4 + - + -
62B MET* 3.0 13.1 + - - +
64B GLN* 1.3 77.8 - - - +
66B GLN* 1.3 62.2 + - + +
68B LEU* 3.1 8.8 + - - -
69B GLY 3.3 0.5 + - - -
70B HIS* 2.9 50.1 + + + +
72B VAL* 5.3 1.8 - - + -
190B VAL* 4.5 13.7 - - + -
192B MET* 4.2 11.9 - - - -
219B PHE* 3.9 30.3 - + - -
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Residues in contact with GLN 66 (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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62B MET 3.0 14.3 + - - +
63B ARG* 3.1 16.3 + - - +
65B PHE* 1.3 77.6 - - - +
67B GLU* 1.3 57.4 + - - +
69B GLY* 2.9 20.3 + - - -
70B HIS 3.4 9.9 - - - +
72B VAL* 3.5 26.2 - - + +
116B LEU* 3.5 13.9 - - - +
117B ARG* 2.8 60.1 + - + +
122B LEU* 3.1 41.5 + - + +
123B PHE* 4.0 1.8 - - - +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 6.2 0.3 - - - -
63B ARG* 2.7 54.5 + - + +
64B GLN* 3.2 8.0 + - - +
66B GLN* 1.3 75.5 - - - +
68B LEU* 1.3 61.7 + - + +
69B GLY 3.2 1.4 + - - -
117B ARG* 3.0 28.7 + - - +
307B PRO* 3.9 30.9 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.8 41.3 - - + +
11B ALA* 4.1 18.8 - - + +
14B LEU* 4.5 13.0 - - + -
15B LEU* 3.9 36.8 - - + -
64B GLN* 3.1 17.5 + - + +
65B PHE* 3.5 9.6 - - - +
66B GLN 3.1 1.0 - - - -
67B GLU* 1.3 80.0 - - + +
69B GLY* 1.3 59.7 + - - +
70B HIS* 3.6 19.2 + - + +
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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