Contacts of the helix formed by residues 57 - 74 (chain B) in PDB entry 1II7
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.9 19.1 - - - +
22B GLU* 5.5 0.7 + - - -
55B ARG 3.7 0.8 + - - -
56B PRO* 1.3 76.4 - - - +
58B PRO* 1.3 75.3 - - - +
59B GLY* 3.4 4.7 + - - -
60B THR* 3.2 24.3 + - - -
61B LEU* 3.0 23.1 + - - +
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER 3.7 22.2 - - - +
55A ARG* 4.5 4.7 - - - -
56A PRO* 4.7 4.7 - - + -
61A LEU* 6.2 1.1 - - + -
88A THR* 4.9 3.6 - - + -
92A PRO* 3.4 20.0 - - + +
93A SER* 3.5 15.9 - - - +
94A VAL* 3.5 27.8 - - + +
97A LEU* 3.9 19.6 - - + +
56B PRO 4.6 0.9 - - - +
57B SER* 1.3 88.8 - - - +
59B GLY* 1.3 56.8 + - - +
61B LEU* 3.5 5.3 + - + +
62B LYS* 2.9 30.2 + - - +
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 3.6 31.4 + - - -
57B SER* 3.1 6.0 + - - -
58B PRO* 1.3 77.4 - - - +
60B THR* 1.3 63.5 + - - +
62B LYS* 3.3 4.6 + - - +
63B LYS* 3.1 21.8 + - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.9 6.4 - - + +
12B GLY* 3.6 35.6 - - - +
22B GLU* 4.0 9.6 + - - -
51B PHE* 3.7 27.6 - - + -
56B PRO* 4.0 5.5 - - + +
57B SER* 3.1 26.3 + - - -
59B GLY* 1.3 75.2 - - - +
61B LEU* 1.3 58.9 + - - +
63B LYS* 3.1 7.9 + - + +
64B ALA* 2.9 26.9 + - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 6.3 1.1 - - + -
61A LEU* 3.5 32.3 - - + -
97A LEU* 4.1 15.7 - - + -
51B PHE* 4.3 4.9 - - + -
56B PRO* 3.6 24.7 - - + +
57B SER 3.0 19.3 + - - +
58B PRO* 3.6 8.1 - - + +
60B THR* 1.3 76.4 - - - +
62B LYS* 1.3 58.2 + - - +
64B ALA* 3.3 4.0 + - - +
65B ILE* 2.9 40.0 + - + +
94B VAL* 3.3 34.3 - - + -
97B LEU* 4.7 9.6 - - + -
98B LEU* 5.3 5.6 - - + -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 4.6 23.4 - - + +
96A ASN* 5.2 6.5 - - - +
97A LEU* 3.8 16.6 - - + +
100A ASP* 3.0 36.7 + - - +
58B PRO 2.9 18.5 + - - +
59B GLY* 3.5 7.2 - - - +
60B THR 3.2 0.2 - - - -
61B LEU* 1.3 78.1 - - - +
63B LYS* 1.3 58.7 + - - +
65B ILE* 3.6 6.4 + - + +
66B ALA* 3.2 22.3 + - - +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 5.6 3.4 - - + -
26B ALA* 3.8 34.3 - - + -
27B GLU* 5.4 2.9 + - - +
30B LYS* 5.4 7.5 - - - +
59B GLY 3.1 12.7 + - - +
60B THR* 3.5 10.1 - - + +
62B LYS* 1.3 73.9 - - - +
64B ALA* 1.3 61.1 + - - +
66B ALA* 3.2 7.8 + - + +
67B LEU* 2.9 58.5 + - + +
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Residues in contact with ALA 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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11B LEU* 3.7 20.3 - - + +
29B PHE* 5.7 0.2 - - - -
50B LEU* 5.8 0.2 - - + -
51B PHE* 3.4 35.0 - - + -
60B THR 2.9 14.5 + - - +
61B LEU* 3.6 4.5 - - - +
63B LYS* 1.3 77.6 - - - +
65B ILE* 1.3 56.3 + - - +
67B LEU* 3.3 3.3 + - - +
68B LEU* 2.8 45.1 + - + +
98B LEU* 5.0 2.7 - - + -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.4 6.5 - - + -
101A PHE* 3.5 38.4 - - + -
61B LEU* 2.9 27.9 + - + +
62B LYS* 3.7 6.3 - - + +
64B ALA* 1.3 76.7 - - - +
66B ALA* 1.3 62.8 + - - +
68B LEU* 3.4 2.3 + - - +
69B GLN* 3.2 39.5 + - + +
98B LEU* 4.1 18.2 - - + -
101B PHE* 3.8 13.9 - - + -
103B LEU* 4.1 15.2 - - + +
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Residues in contact with ALA 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 LYS 3.2 15.9 + - - +
63B LYS* 3.7 11.7 - - + +
65B ILE* 1.3 80.9 - - - +
67B LEU* 1.3 65.1 + - + +
69B GLN* 3.1 27.2 + - - +
70B ILE* 4.0 4.9 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.4 5.4 - - + -
26B ALA* 3.4 25.6 - - - +
29B PHE* 3.6 31.6 - - + -
30B LYS* 3.9 32.3 - - + +
33B LEU* 3.4 11.9 - - + +
63B LYS* 2.9 53.5 + - + +
64B ALA 3.7 4.3 - - - +
66B ALA* 1.3 78.8 - - + +
68B LEU* 1.3 57.9 + - - +
69B GLN 3.0 0.2 - - - -
70B ILE* 3.1 32.7 + - + +
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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
----------------------------------------------------------
29B PHE* 4.1 27.1 - - + -
33B LEU* 4.9 1.3 - - + -
46B ILE* 4.8 2.5 - - + -
50B LEU* 4.6 7.0 - - + -
64B ALA* 2.8 23.0 + - + +
65B ILE 3.9 4.7 - - - +
67B LEU* 1.3 73.8 - - - +
69B GLN* 1.3 62.1 + - - +
70B ILE 3.1 1.0 + - - -
71B PRO* 3.3 19.1 - - + +
72B LYS* 3.3 12.7 + - - +
78B VAL* 4.5 15.9 - - + -
98B LEU* 3.6 34.3 - - + -
103B LEU* 4.0 34.8 - - + +
104B VAL* 3.9 18.4 - - + -
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Residues in contact with GLN 69 (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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65B ILE* 3.2 35.1 + - + +
66B ALA* 3.1 18.8 + - - +
67B LEU 3.0 1.4 - - - -
68B LEU* 1.3 75.4 - - - +
70B ILE* 1.3 53.6 + - + +
72B LYS* 3.7 12.6 - - - +
73B GLU* 2.7 60.6 + - + +
103B LEU* 3.6 19.8 - - - +
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Residues in contact with ILE 70 (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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30B LYS* 3.9 37.2 - - + +
33B LEU* 4.3 13.5 - - + -
34B GLU* 4.2 22.0 - - + +
37B VAL* 3.8 20.4 - - + -
66B ALA 4.4 4.3 - - - +
67B LEU* 3.1 21.5 + - + +
69B GLN* 1.3 81.0 - - + +
71B PRO* 1.3 72.0 - - + +
73B GLU* 3.3 6.3 + - - +
74B HIS* 3.2 27.8 - - + +
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Residues in contact with PRO 71 (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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33B LEU* 4.1 18.8 - - + -
37B VAL* 4.6 8.3 - - + -
44B ILE* 3.8 20.0 - - + -
67B LEU 3.5 7.0 - - - +
68B LEU* 3.3 18.2 - - + +
70B ILE* 1.3 97.9 - - + +
72B LYS* 1.3 61.2 + - - +
74B HIS* 3.1 7.7 + - - +
76B ILE* 2.9 45.5 + - + +
78B VAL* 3.8 19.1 - - + -
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Residues in contact with LYS 72 (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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68B LEU 3.3 17.2 + - - +
69B GLN* 3.5 21.3 - - - +
70B ILE 3.2 0.4 - - - -
71B PRO* 1.3 79.7 - - - +
73B GLU* 1.3 66.4 + - - +
75B SER* 3.0 16.8 + - - +
76B ILE 4.6 3.1 + - - +
101B PHE 4.9 2.7 + - - -
102B GLY* 2.8 37.8 + - - +
103B LEU* 4.2 11.2 - - + +
105B TYR* 5.4 4.9 + - - -
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Residues in contact with GLU 73 (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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69B GLN* 2.7 49.4 + - + +
70B ILE* 3.6 9.6 - - - +
71B PRO 3.2 0.4 - - - -
72B LYS* 1.3 80.6 - - - +
74B HIS* 1.3 70.7 + - + +
75B SER* 3.7 1.9 + - - -
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.5 33.2 - - + +
70B ILE* 3.2 26.7 - - - +
71B PRO 3.1 7.0 + - - +
73B GLU* 1.3 85.5 + - + +
75B SER* 1.3 73.2 + - - +
76B ILE* 3.1 19.3 + - + +
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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