Contacts of the helix formed by residues 88 - 104 (chain B) in PDB entry 2PID
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 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 1.3 75.3 - - - +
89B VAL* 1.3 64.3 + - - +
90B GLY* 2.9 37.0 + - - -
91B HIS* 3.0 49.8 + + - +
92B LEU 3.3 7.3 + - - -
289B ALA* 5.2 9.2 - - + -
290B VAL 3.3 21.3 - - - +
291B TRP* 3.9 24.9 - + + -
292B LEU* 3.7 12.1 - - - +
384B YSA 3.9 13.6 + + - -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 1.3 74.8 + - - +
90B GLY* 1.3 64.8 + - - +
92B LEU* 3.2 20.9 - - + +
93B LEU 3.8 0.5 + - - -
274B ILE* 5.3 2.5 - - + -
275B THR 5.0 7.0 - - - +
290B VAL* 3.1 42.8 + - + +
292B LEU* 3.7 8.2 - - + +
302B LEU* 3.9 6.3 - - + -
305B PHE* 4.0 19.7 - - + -
306B PHE* 3.6 24.9 - - + -
321B PHE* 3.6 29.5 - - + -
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 2.9 18.3 + - - -
89B VAL* 1.3 76.2 - - - +
91B HIS* 1.3 63.1 + - - +
92B LEU 3.1 0.7 + - - -
93B LEU* 3.2 11.4 + - - +
94B ALA 4.1 0.5 + - - -
274B ILE* 5.2 2.7 - - - -
275B THR 6.4 0.9 - - - -
321B PHE* 5.7 0.9 - - - -
384B YSA 3.3 51.7 + - - -
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.7 12.2 - + + -
81B ASP 5.3 5.6 - - - -
83B THR* 5.9 2.5 - - - -
84B ALA* 6.4 0.2 - - + -
86B SER 4.6 4.3 - - - -
87B LEU* 3.4 34.5 - - + +
88B HIS* 3.0 52.6 + + - +
90B GLY* 1.3 76.1 - - - +
92B LEU* 1.3 63.8 + - - +
94B ALA* 3.1 7.2 + - - +
95B LEU* 3.0 18.7 + - - +
291B TRP* 5.4 0.4 - + - -
384B YSA 3.2 56.9 + + - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS 3.3 5.3 + - - +
89B VAL* 3.2 19.3 + - + +
90B GLY 3.0 0.8 - - - -
91B HIS* 1.3 80.7 - - - +
93B LEU* 1.3 51.5 + - - +
95B LEU* 3.1 21.0 + - + +
96B LEU* 2.7 50.8 + - + +
151B LEU* 4.5 4.9 - - + -
292B LEU* 4.0 24.6 - - + +
306B PHE* 4.9 1.8 - - + -
321B PHE* 4.0 16.8 - - + +
353B VAL* 3.8 28.7 - - + -
356B LEU* 4.6 17.5 - - + -
357B VAL* 4.1 13.5 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 16.6 - - + +
89B VAL 3.8 1.7 + - - +
90B GLY 3.2 12.6 + - - +
91B HIS 3.2 0.6 - - - -
92B LEU* 1.3 77.6 - - - +
94B ALA* 1.3 58.4 + - - +
96B LEU* 3.2 5.5 + - + +
97B GLY* 2.9 24.6 + - - -
271B VAL* 4.3 5.9 - - + +
272B PRO* 3.2 33.7 - - + +
274B ILE* 3.6 22.7 - - + -
320B LEU* 3.8 36.1 - - + +
321B PHE* 3.7 33.2 - - + -
384B YSA 4.2 7.6 - - + -
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Residues in contact with ALA 94 (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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78B CYS* 3.8 22.2 - - - -
80B PHE* 4.0 5.4 - - + -
90B GLY 4.1 0.6 + - - -
91B HIS 3.1 9.9 + - - +
93B LEU* 1.3 78.1 - - - +
95B LEU* 1.3 62.4 + - - +
97B GLY 3.1 8.7 + - - -
98B LEU* 3.3 12.1 + - - +
242B LEU* 3.3 20.5 - - + +
271B VAL* 4.3 9.7 - - + +
384B YSA 3.6 29.2 - - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 4.1 12.9 - - + -
87B LEU* 5.5 1.6 - - + -
91B HIS 3.0 12.5 + - - +
92B LEU* 3.1 16.4 + - + +
94B ALA* 1.3 78.5 - - - +
96B LEU* 1.3 62.0 + - - +
98B LEU* 3.0 18.7 + - + +
99B PHE* 3.0 49.9 + - + -
148B LEU* 4.2 16.4 - - + +
151B LEU* 3.6 32.3 - - + -
168B PHE* 3.8 31.9 - - + -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.4 9.4 - - + -
92B LEU* 2.7 35.2 + - + +
93B LEU* 3.2 9.8 + - + +
95B LEU* 1.3 74.9 - - - +
97B GLY* 1.3 62.8 + - - +
99B PHE* 3.2 7.8 + - + +
100B HIS* 3.0 33.3 + - + +
320B LEU 3.3 22.2 - - - +
321B PHE* 3.5 36.1 - - + +
322B THR 5.9 0.2 - - - -
323B PHE* 3.8 25.8 - - + -
356B LEU* 3.8 25.6 - - + -
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.9 6.9 - - - +
48B PHE* 3.7 24.1 - - - -
93B LEU 2.9 13.1 + - - -
94B ALA 3.1 4.7 + - - -
95B LEU 3.1 0.6 - - - -
96B LEU* 1.3 77.6 - - - +
98B LEU* 1.3 62.3 + - - +
100B HIS* 3.3 3.1 + - - +
101B LEU* 3.1 24.4 + - - +
242B LEU* 4.1 11.9 - - - -
271B VAL* 4.8 0.9 - - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.1 30.5 - - + +
77B TYR 4.2 0.2 - - - -
78B CYS* 3.9 26.2 - - + +
80B PHE* 4.4 2.7 - - + -
94B ALA 3.3 10.8 + - - +
95B LEU* 3.0 27.4 + - + +
97B GLY* 1.3 74.7 - - - +
99B PHE* 1.3 53.6 + - + +
101B LEU* 2.9 9.3 + - + +
102B GLN* 2.8 32.0 + - - +
108B VAL* 3.3 39.6 - - + +
109B ILE 3.6 17.0 - - - +
110B ALA* 4.3 7.2 - - + -
168B PHE* 4.7 0.4 - - + -
242B LEU* 4.5 4.7 - - + +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 5.8 0.2 - - + -
95B LEU* 3.0 44.6 + - + -
96B LEU* 3.5 24.7 - - + +
98B LEU* 1.3 76.3 - - - +
100B HIS* 1.3 57.6 + - - +
102B GLN* 3.2 13.1 + - - +
103B ARG* 2.9 36.9 + - - +
151B LEU* 3.9 4.9 - - + -
152B ALA* 3.9 22.9 - - - -
155B HIS* 3.5 45.5 - + + +
168B PHE* 3.6 30.3 - + - -
323B PHE* 4.0 7.2 - + + -
356B LEU* 4.2 16.2 - - + -
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Residues in contact with HIS 100 (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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38B LEU* 4.0 6.7 - - + +
42B GLN* 3.3 47.1 + - + +
45B ARG* 4.1 14.3 + - - -
47B LEU* 3.4 19.6 - - + +
48B PHE* 4.7 2.5 - - + -
96B LEU* 3.0 27.9 + - + -
97B GLY 3.6 7.6 - - - +
99B PHE* 1.3 75.7 - - - +
101B LEU* 1.3 63.3 + - - +
103B ARG* 3.4 17.5 + - - +
104B ALA* 3.4 13.5 + - - +
163B ARG* 5.3 0.9 + - - -
320B LEU 5.1 2.9 - - - -
322B THR 4.4 9.8 + - - -
323B PHE* 3.5 34.5 - + - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.2 36.6 - - + -
48B PHE* 3.9 15.7 - - + -
65B PHE* 3.8 20.2 - - + -
76B ILE* 3.5 43.5 - - + -
97B GLY 3.1 15.7 + - - +
98B LEU* 2.9 13.7 + - - +
100B HIS* 1.3 75.3 - - - +
102B GLN* 1.3 62.4 + - - +
104B ALA 3.2 9.2 + - - -
106B HIS* 3.3 25.3 + - + -
108B VAL* 4.1 6.5 - - + -
242B LEU* 4.5 12.8 - - + -
269B ILE* 4.6 3.6 - - + -
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Residues in contact with GLN 102 (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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98B LEU 2.8 15.0 + - - +
99B PHE* 3.2 19.4 + - - +
101B LEU* 1.3 78.5 - - - +
103B ARG* 1.3 61.1 + - - +
105B GLY 3.1 2.9 + - - -
106B HIS 3.4 11.0 - - - +
108B VAL* 4.0 7.5 - - + +
152B ALA* 5.9 0.2 - - - +
155B HIS* 4.0 9.1 + - + -
156B GLN* 3.4 21.8 + - - +
165B TRP* 3.3 13.9 - - + -
166B GLY 2.9 57.9 + - - +
167B SER* 3.7 4.3 - - - +
168B PHE* 3.7 36.0 + - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE 2.9 27.6 + - - +
100B HIS* 3.7 11.5 - - - +
101B LEU 3.2 0.2 - - - -
102B GLN* 1.3 76.5 - - - +
104B ALA* 1.3 57.1 + - - +
105B GLY 3.1 3.7 + - - -
155B HIS* 3.0 37.1 + - + -
159B PHE* 2.9 32.9 + - - +
161B ASP* 4.0 21.4 + - - +
163B ARG* 3.5 36.0 + - - +
164B SER 4.3 1.2 - - - +
165B TRP* 3.5 35.2 - - + +
323B PHE* 3.7 43.1 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.1 23.3 - - + -
67B ARG* 4.8 7.6 - - - +
72B PHE* 3.7 16.5 - - - -
100B HIS 3.4 9.7 + - - +
101B LEU 3.2 9.6 + - - +
102B GLN 3.2 1.0 - - - -
103B ARG* 1.3 76.9 - - - +
105B GLY* 1.3 57.8 + - - +
106B HIS* 3.6 13.7 + - + +
163B ARG* 4.0 16.8 - - - +
164B SER 4.8 0.9 - - - -
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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