Contacts of the strand formed by residues 112 - 124 (chain B) in PDB entry 1PH7
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 LEU 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PHE* 4.1 16.6 - - + -
97B LEU* 5.9 2.0 - - + -
98B ARG 3.8 2.9 - - - +
99B ARG* 4.3 22.2 - - + -
102B SER* 3.9 0.8 + - - -
108B SER* 3.3 2.6 - - - -
109B TYR 2.9 31.2 + - - +
110B ALA 3.7 7.0 - - - +
111B ASN* 1.3 87.5 - - - +
113B GLU* 1.3 61.9 + - - +
139B PHE* 3.7 5.8 - - - -
148B ILE* 4.0 9.8 - - + +
151B PHE* 3.7 31.4 - - + -
152B ARG* 3.7 25.6 - - + +
203B PHE* 4.3 15.3 - - + -
205B PHE* 4.4 12.3 - - + -
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Residues in contact with GLU 113 (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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22B PHE* 4.8 3.6 - - - -
62B TYR* 2.8 28.3 + - - -
97B LEU* 3.8 0.7 - - - +
98B ARG* 2.7 44.4 + - + +
100B VAL* 3.5 22.0 - - + +
105B VAL* 3.7 9.4 - - - +
107B THR* 3.0 28.4 + - - +
108B SER* 3.6 12.3 - - - -
112B LEU* 1.3 74.5 - - - +
114B ALA* 1.3 66.2 + - - +
115B ARG* 2.8 40.4 + - + -
139B PHE* 4.2 1.8 - - - -
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Residues in contact with ALA 114 (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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18B TYR* 3.0 46.0 + - + -
21B LEU* 4.4 14.8 - - + -
22B PHE* 3.6 25.9 - - + -
95B LEU* 6.2 0.4 - - + -
96B GLU 3.9 4.7 - - - -
97B LEU* 4.5 3.8 - - + +
112B LEU 4.3 0.2 - - - -
113B GLU* 1.3 75.3 - - - +
115B ARG* 1.3 58.2 + - - +
139B PHE* 3.5 13.5 - - + -
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Residues in contact with ARG 115 (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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18B TYR* 4.3 1.3 - - - -
62B TYR* 3.2 45.9 + - + -
95B LEU* 3.3 8.5 - - - +
96B GLU* 2.9 39.9 + - + +
98B ARG* 4.0 32.7 - - + +
100B VAL* 4.8 6.7 - - - +
105B VAL* 5.8 3.4 - - - +
113B GLU* 2.8 33.5 + - + -
114B ALA* 1.3 73.4 - - - +
116B LEU* 1.3 60.8 + - - +
117B ILE* 3.7 16.5 + - + +
210B THR 5.3 0.6 + - - -
212B THR* 3.3 31.1 - - - +
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Residues in contact with LEU 116 (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 PHE* 5.2 6.1 - - + -
17B LEU* 6.0 0.2 - - + -
18B TYR* 3.2 24.2 + - + +
39B LEU* 4.5 10.8 - - + -
52B VAL* 5.0 3.4 - - + -
59B VAL* 4.4 13.0 - - + -
60B ALA 4.7 1.4 + - - +
61B PRO* 3.5 27.3 - - + +
62B TYR* 2.9 28.2 + - - -
90B ILE* 4.3 13.5 - - + -
93B TRP* 3.8 33.2 - - + -
95B LEU* 3.5 24.2 - - + -
115B ARG* 1.3 71.0 - - - +
117B ILE* 1.3 60.5 + - - +
118B VAL* 3.4 6.3 + - + -
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Residues in contact with ILE 117 (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 TYR* 3.6 17.9 - - + +
64B THR* 3.6 28.3 - - + -
93B TRP* 3.3 5.8 - - - +
94B SER* 2.8 52.3 + - - +
96B GLU* 3.5 32.8 - - + +
115B ARG* 4.0 19.5 - - + +
116B LEU* 1.3 70.3 - - - +
118B VAL* 1.3 60.8 + - - +
119B HIS* 3.8 11.8 + - + -
210B THR* 3.6 28.0 - - + +
212B THR* 5.2 4.3 - - + -
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Residues in contact with VAL 118 (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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61B PRO* 3.7 26.0 - - + -
62B TYR 3.1 6.5 + - - -
63B PHE* 3.6 26.2 - - + -
64B THR* 3.3 20.7 + - - +
67B ALA* 3.3 12.8 - - - +
90B ILE* 3.5 45.1 - - + -
92B ASN 3.9 2.0 - - - -
93B TRP* 4.5 0.9 - - - +
116B LEU* 3.9 8.1 - - + +
117B ILE* 1.3 73.2 - - - +
119B HIS* 1.3 61.2 + - - +
120B SER 3.7 16.6 - - - +
121B PHE* 4.0 5.8 - - + -
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Residues in contact with HIS 119 (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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64B THR* 4.0 14.8 + - + +
66B GLU* 4.2 6.4 - - + +
67B ALA* 3.1 25.4 + - - -
70B GLU* 4.4 2.4 - - - +
92B ASN* 2.7 56.5 + - - +
93B TRP* 4.0 7.9 - - - -
94B SER* 3.0 27.8 + - - -
117B ILE* 4.1 15.9 + - + -
118B VAL* 1.3 73.0 - - - +
120B SER* 1.3 60.2 + - - +
210B THR* 5.7 2.0 - - - -
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Residues in contact with SER 120 (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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67B ALA* 4.2 6.7 - - - +
70B GLU* 2.5 41.9 + - - -
90B ILE* 3.6 6.9 - - - +
91B ASN* 3.4 25.8 + - - +
92B ASN* 3.4 15.7 + - - -
118B VAL* 3.5 2.3 - - - +
119B HIS* 1.3 81.7 - - - +
121B PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 121 (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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63B PHE* 3.6 43.7 - + - -
67B ALA* 4.3 15.2 + - + -
68B VAL 4.5 0.2 - - - -
70B GLU* 5.0 1.9 + - - +
71B PHE* 3.0 72.1 - + + +
75B PHE* 5.0 1.7 - - - -
80B ILE* 3.5 31.4 - - + -
83B LEU* 4.1 7.2 - - + -
88B ILE* 3.9 22.9 - - + -
89B VAL 3.0 14.4 - - - +
90B ILE* 4.0 14.8 - - + -
91B ASN* 4.9 0.7 - - - +
118B VAL* 4.0 2.9 - - + -
120B SER* 1.3 81.2 + - - +
122B LYS* 1.3 59.4 + - - +
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Residues in contact with LYS 122 (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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71B PHE* 4.3 1.1 - - - -
74B LYS* 5.8 4.2 - - + +
75B PHE* 3.2 34.5 - - + -
88B ILE* 3.4 3.0 - - - -
89B VAL* 2.8 46.6 + - + +
91B ASN* 5.2 10.2 - - - +
121B PHE* 1.3 74.1 - - - +
123B PRO* 1.3 71.6 - - + +
124B ASN* 3.4 12.0 + - - +
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Residues in contact with PRO 123 (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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71B PHE* 3.2 35.7 - - + -
75B PHE* 3.5 38.5 - - + -
78B VAL* 4.4 9.6 - - + -
83B LEU* 4.2 17.0 - - + -
87B VAL 3.9 5.6 - - - +
88B ILE* 4.4 4.5 - - + -
122B LYS* 1.3 86.2 - - + +
124B ASN* 1.3 57.4 + - - +
125B LEU* 2.7 27.0 + - + +
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Residues in contact with ASN 124 (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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40B LYS* 4.4 5.9 - - - +
86B LYS* 5.4 0.8 - - - +
87B VAL* 3.1 28.9 + - + +
89B VAL* 3.2 31.5 - - + +
122B LYS* 3.4 12.5 + - - +
123B PRO* 1.3 66.9 - - - +
125B LEU* 1.3 66.4 + - - +
126B GLN 3.6 0.3 + - - -
127B GLU* 2.7 45.3 + - + +
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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
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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