Contacts of the strand formed by residues 87 - 99 (chain B) in PDB entry 1PH2
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 VAL 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B LYS* 4.3 14.6 - - + -
41B CYS 3.4 20.2 - - - +
42B TYR* 4.3 8.3 - - + +
43B VAL 4.4 0.9 - - - +
86B LYS* 1.3 74.6 - - - +
88B ILE* 1.3 77.8 + - - +
123B PRO* 3.8 2.3 - - - +
124B ASN* 3.2 37.1 + - + +
126B GLN 5.9 0.2 - - - +
127B GLU* 3.1 49.9 + - + +
129B LEU* 4.9 9.9 - - + -
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Residues in contact with ILE 88 (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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39B LEU 3.8 0.3 - - - +
41B CYS* 3.1 41.3 + - - +
43B VAL* 3.7 15.5 - - + -
50B PHE* 3.9 30.1 - - + -
52B VAL* 4.0 10.1 - - + -
61B PRO* 5.7 0.2 - - + -
63B PHE* 4.8 2.7 - - + -
83B LEU* 4.1 23.8 - - + -
87B VAL* 1.3 80.9 - - - +
89B VAL* 1.3 66.5 + - - +
90B ILE* 4.5 15.5 - - + -
121B PHE* 4.1 21.5 - - + -
122B LYS 3.4 7.4 - - - +
123B PRO* 4.2 11.0 - - + -
124B ASN 4.4 0.4 - - - +
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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
----------------------------------------------------------
38B PRO* 4.6 9.9 - - + -
39B LEU 3.6 9.2 - - - +
40B LYS* 4.4 22.7 - - + +
87B VAL* 5.3 0.7 - - + -
88B ILE* 1.3 78.5 - - - +
90B ILE* 1.3 62.5 + - - +
91B ASN* 3.4 25.0 + - - +
121B PHE* 3.1 3.8 - - - -
122B LYS* 2.8 44.3 + - + +
124B ASN* 3.4 32.8 - - + +
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Residues in contact with ILE 90 (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 PRO* 3.4 0.3 - - - +
39B LEU* 2.9 42.7 + - + +
41B CYS* 3.8 24.7 - - - -
52B VAL* 5.3 0.9 - - + -
61B PRO* 5.0 3.8 - - + -
63B PHE* 5.8 0.2 - - + -
88B ILE* 4.5 13.0 - - + -
89B VAL* 1.3 70.1 - - - +
91B ASN* 1.3 59.8 + - - +
92B ASN 4.1 2.5 - - - +
93B TRP* 3.4 38.4 - - + -
116B LEU* 3.9 25.6 - - + -
118B VAL* 3.7 29.6 - - + -
120B SER 3.5 5.8 - - - +
121B PHE* 3.9 10.5 - - + -
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Residues in contact with ASN 91 (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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36B LYS 5.5 1.6 - - - +
37B LYS 5.4 0.3 - - - -
38B PRO* 3.9 27.5 - - + +
89B VAL* 3.4 27.2 + - - +
90B ILE* 1.3 74.9 - - - +
92B ASN* 1.3 58.8 + - + +
93B TRP* 4.0 6.0 + - - -
120B SER* 2.8 23.4 + - - +
122B LYS* 4.3 19.0 - - - +
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Residues in contact with ASN 92 (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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90B ILE* 4.1 1.2 - - - +
91B ASN* 1.3 80.0 - - + +
93B TRP* 1.3 62.1 + - - +
118B VAL* 4.1 0.3 - - - -
119B HIS* 2.7 62.2 + - + +
120B SER* 3.2 18.9 + - - +
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Residues in contact with TRP 93 (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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17B LEU* 3.7 19.1 - - + -
28B PHE* 3.6 30.2 - + - -
35B LEU 3.3 27.1 - - - -
36B LYS* 3.7 16.3 + - - +
37B LYS 3.3 26.2 + - - -
38B PRO* 4.2 0.4 - - - +
39B LEU* 3.4 24.5 - - + +
90B ILE* 3.4 41.0 + - + -
91B ASN 4.2 4.4 + - - -
92B ASN* 1.3 77.9 + - - +
94B SER* 1.3 69.9 + - - +
95B LEU* 4.0 13.9 - - + -
116B LEU* 3.8 19.5 - - + -
117B ILE 3.0 13.5 - - - +
119B HIS* 4.0 4.7 - - - -
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Residues in contact with SER 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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28B PHE* 3.5 20.4 - - - -
93B TRP* 1.3 77.8 - - - +
95B LEU* 1.3 63.8 + - - +
96B GLU* 5.4 1.4 + - - -
115B ARG 3.5 0.7 - - - +
116B LEU* 3.6 4.3 - - - +
117B ILE* 2.7 56.8 + - - +
119B HIS* 3.4 13.5 + - - -
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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
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17B LEU* 4.0 38.6 - - + +
18B TYR* 3.7 23.6 - - + -
21B LEU* 3.7 22.9 - - + +
26B GLY 5.0 0.3 - - - +
28B PHE* 3.2 52.0 + - + +
31B VAL* 5.9 1.6 - - + -
93B TRP* 4.0 8.7 - - + -
94B SER* 1.3 78.7 - - - +
96B GLU* 1.3 63.8 + - - +
115B ARG 3.2 17.0 - - - +
116B LEU* 3.7 21.3 - - + -
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Residues in contact with GLU 96 (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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21B LEU* 4.1 3.3 - - - +
26B GLY 5.1 3.8 - - - -
94B SER* 5.4 0.9 + - - -
95B LEU* 1.3 75.4 - - - +
97B LEU* 1.3 64.7 + - - +
98B ARG* 3.7 11.3 - - + +
113B GLU 3.7 0.2 - - - +
114B ALA* 3.6 0.7 - - - -
115B ARG* 2.8 36.0 + - + +
117B ILE* 3.9 20.8 - - + +
208B GLY* 3.4 33.8 - - - +
209B ASN 4.0 5.7 + - - +
210B THR* 2.9 40.3 + - - +
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Residues in contact with LEU 97 (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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21B LEU* 3.3 38.1 - - + -
22B PHE* 3.8 31.4 - - + -
26B GLY* 3.8 24.9 + - - +
96B GLU* 1.3 74.6 - - - +
98B ARG* 1.3 62.8 + - - +
112B LEU* 5.6 2.7 - - + -
113B GLU 3.3 7.2 - - - +
114B ALA* 4.0 14.4 - - + -
151B PHE* 3.9 22.4 - - + -
205B PHE* 3.7 27.4 - - + -
207B GLU* 3.8 3.1 - - - -
208B GLY 3.1 26.0 + - - +
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Residues in contact with ARG 98 (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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96B GLU* 3.7 14.8 - - - +
97B LEU* 1.3 77.7 - - - +
99B ARG* 1.3 66.9 + - - +
100B VAL* 3.5 9.2 + - + +
112B LEU* 3.7 4.3 - - - +
113B GLU* 2.8 37.7 + - - +
115B ARG* 3.8 51.2 - - + +
205B PHE* 5.3 0.9 - - - -
207B GLU* 3.6 27.0 + - - +
208B GLY 2.8 30.2 + - - -
209B ASN* 4.2 10.1 - - - +
210B THR 5.7 1.1 - - - +
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Residues in contact with ARG 99 (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 ARG* 1.3 76.2 + - - +
100B VAL* 1.3 63.9 + - - +
111B ASN* 3.7 11.1 + - - +
112B LEU* 4.7 6.0 - - + +
199B GLU* 3.1 29.3 + - - +
200B PHE 4.1 2.4 + - - -
201B SER* 3.0 41.0 + - - +
203B PHE* 5.1 11.2 - - - -
205B PHE* 4.2 18.8 - - + -
207B GLU* 2.9 34.6 + - - +
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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
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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