Contacts of the strand formed by residues 42 - 52 (chain B) in PDB entry 1GP9
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 PHE 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.8 21.0 + - - +
40B HIS 3.3 3.3 + - - -
41B GLU* 1.3 86.5 - - + +
43B LYS* 1.3 61.6 + - - +
44B LYS* 3.3 6.2 + - - +
71B ALA* 3.5 35.0 - - + -
74B CYS* 3.9 24.7 - - + -
75B THR* 3.1 28.5 - - - -
86B ALA* 5.2 0.2 - - - -
87B PHE* 4.1 6.5 - + - -
119B TYR* 3.7 30.2 - - + -
120B GLU 3.1 7.4 - - - +
121B ASN* 3.2 46.9 - - + -
122B LYS* 4.6 2.4 - - - +
139B THR* 5.7 1.3 - - - -
176B TYR* 5.2 0.7 + - - -
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Residues in contact with LYS 43 (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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42B PHE* 1.3 68.5 - - - +
44B LYS* 1.3 67.6 + - - +
45B SER* 4.5 3.7 + - - +
104B MET* 6.2 0.4 - - - -
118B LEU 3.7 0.9 - - - +
119B TYR* 3.6 1.5 - - - -
120B GLU* 2.7 50.2 + - + +
122B LYS* 5.2 2.0 - - + +
125B ILE* 4.2 17.6 - - + +
137B LYS* 2.7 39.0 + - - +
139B THR* 4.0 17.6 - - + +
171B ASP* 2.6 37.6 + - - -
173B GLN* 6.2 0.2 - - - -
176B TYR* 4.0 31.6 - - + +
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE 3.3 5.2 + - - +
43B LYS* 1.3 79.2 - - - +
45B SER* 1.3 70.2 + - - +
46B ALA* 4.2 14.0 - - - +
117B ASP* 3.8 31.1 + - + -
118B LEU 3.1 9.6 - - - +
119B TYR* 3.8 35.6 + - + +
176B TYR* 5.0 2.9 + - - -
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Residues in contact with SER 45 (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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43B LYS* 4.5 4.3 + - - +
44B LYS* 1.3 78.6 + - - +
46B ALA* 1.3 66.1 + - - +
48B THR* 3.6 17.9 - - - -
110B LYS* 5.2 6.5 + - - -
118B LEU* 2.8 45.7 + - - +
120B GLU* 4.3 14.2 + - - -
1210B EPE 6.0 7.0 - - - -
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Residues in contact with ALA 46 (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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44B LYS* 4.2 15.5 - - - +
45B SER* 1.3 69.6 - - - +
47B LYS* 1.3 64.0 + - + +
48B THR* 2.7 11.6 + - - -
117B ASP* 2.9 16.2 - - - +
1210B EPE 2.4 31.1 + - - -
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Residues in contact with LYS 47 (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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46B ALA* 1.3 77.7 - - + +
48B THR* 1.3 55.7 + - - +
91B LYS* 5.5 1.6 - - - +
112B PHE* 3.6 21.3 - - + -
113B GLY 3.0 29.8 + - - +
114B HIS* 2.8 59.7 + - + +
116B PHE 2.7 17.4 + - - -
117B ASP* 3.1 3.4 + - - +
1210B EPE 3.0 14.2 + - - +
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Residues in contact with THR 48 (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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45B SER* 3.6 19.7 + - - -
46B ALA 2.7 20.0 + - - -
47B LYS* 1.3 75.5 + - - +
49B THR* 1.3 72.4 + - - +
88B VAL* 4.0 0.5 - - - +
110B LYS* 3.7 29.8 - - + +
111B GLU 4.2 5.8 - - - +
116B PHE* 2.9 10.2 + - - +
117B ASP 3.6 4.3 - - - -
118B LEU* 3.3 36.9 + - + +
1210B EPE 2.9 18.3 + - - -
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Residues in contact with THR 49 (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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48B THR* 1.3 74.4 - - - +
50B LEU* 1.3 78.1 + - - +
51B ILE* 5.1 1.8 - - + -
88B VAL* 3.7 22.5 - - - +
97B LEU* 4.4 5.0 - - - +
99B PHE* 4.9 1.4 - - - -
110B LYS* 3.5 8.7 - - - +
111B GLU* 3.3 49.9 + - + +
112B PHE 5.1 0.2 - - - +
116B PHE* 3.7 36.0 - - + +
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Residues in contact with LEU 50 (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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49B THR* 1.3 92.8 + - - +
51B ILE* 1.3 63.8 + - - +
59B ILE* 5.7 1.9 - - - +
86B ALA* 5.0 0.4 - - + -
88B VAL* 4.4 3.0 - - + +
99B PHE* 4.3 21.5 - - + -
101B PHE* 4.0 29.0 - - + +
102B ASN* 3.9 8.7 - - - +
103B SER* 3.9 35.0 - - - +
108B VAL* 4.4 6.3 - - + -
109B LYS 3.8 6.1 - - - +
110B LYS* 3.6 24.0 - - + +
118B LEU* 4.0 31.6 - - + -
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Residues in contact with ILE 51 (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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49B THR* 5.1 2.0 - - + -
50B LEU* 1.3 77.2 - - - +
52B LYS* 1.3 73.5 + - + +
53B ILE* 3.7 4.1 + - + +
101B PHE* 5.4 0.4 - - - -
108B VAL* 3.2 22.1 - - - +
109B LYS* 3.1 21.7 + - + +
110B LYS 5.7 0.2 - - - -
111B GLU* 2.9 46.4 - - + +
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Residues in contact with LYS 52 (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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50B LEU 4.4 0.2 + - - -
51B ILE* 1.3 79.1 - - + +
53B ILE* 1.3 61.7 + - - +
54B ASP 3.0 12.9 + - - +
55B PRO* 3.9 12.7 + - - +
56B ALA 4.7 0.2 + - - -
57B LEU* 2.7 52.2 + - + +
58B LYS* 4.3 10.5 - - - +
59B ILE* 3.7 30.3 - - + +
101B PHE* 4.3 9.1 - - + -
107B GLY 3.6 5.6 - - - -
108B VAL* 4.0 1.8 - - - -
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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