Contacts of the strand formed by residues 55 - 63 (chain B) in PDB entry 4PN6
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 ALA 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.1 16.9 + - + +
54B ASN* 1.4 74.4 - - - +
56B SER* 1.3 57.9 + - - +
57B TRP* 3.8 11.2 - - - +
77B GLU* 3.5 4.3 - - - +
78B SER 2.8 33.0 + - - +
145B MET* 3.6 29.2 - - - -
146B CYS 3.5 7.9 - - - +
147B PRO* 3.8 3.8 - - + -
148B TRP* 3.3 15.6 + - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 5.6 0.4 - - - -
55B ALA* 1.3 72.9 - - - +
57B TRP* 1.3 62.3 + - - +
58B THR* 4.9 2.0 + - - -
75B TYR* 3.3 32.3 - - - -
76B TYR 3.6 4.7 - - - -
77B GLU* 4.3 1.3 - - - -
144B ARG* 3.2 5.4 + - - +
145B MET* 3.4 1.6 - - - -
146B CYS* 2.8 54.3 + - - +
148B TRP* 4.0 11.2 + - - -
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 14.8 - - + -
49B PRO* 3.6 37.7 - - + -
51B VAL* 3.8 12.1 - - + -
53B VAL* 5.5 0.4 - - + -
55B ALA* 3.8 16.2 - - + +
56B SER* 1.3 77.4 - - - +
58B THR* 1.3 61.7 + - - +
59B LEU 4.0 1.1 - - - -
74B SER 3.4 3.5 - - - +
75B TYR* 3.5 0.9 - - - -
76B TYR* 2.7 56.7 + - + +
78B SER* 3.2 25.7 - - - -
84B PRO* 3.7 29.8 - - + +
143B LEU* 3.7 30.7 - - + -
144B ARG 3.7 3.1 - - - -
145B MET* 3.8 23.8 - - + -
168B VAL* 3.6 28.0 - - + -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 4.9 2.1 + - - -
57B TRP* 1.3 70.5 + - - +
59B LEU* 1.3 58.9 + - - +
60B GLU* 3.8 1.1 + - - +
73B THR* 3.5 31.6 - - + +
74B SER 3.6 4.9 - - - +
75B TYR* 3.3 22.2 - - + -
90B ILE* 4.0 17.2 - - + +
142B ARG 3.3 4.5 - - - +
143B LEU* 4.2 0.8 - - - +
144B ARG* 2.8 54.8 + - + +
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Residues in contact with LEU 59 (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 ILE* 5.6 0.7 - - + -
46B CYS* 4.2 13.9 - - + +
48B LEU* 3.7 31.4 - - + -
57B TRP 4.0 0.2 - - - -
58B THR* 1.3 73.5 - - - +
60B GLU* 1.3 59.4 + - - +
61B TRP* 3.6 39.6 + - + +
73B THR* 3.6 5.4 - - - -
74B SER* 3.2 41.1 + - - +
76B TYR* 3.7 22.0 - - + +
123B GLY 4.6 0.4 - - - +
141B CYS* 4.0 16.8 - - + -
142B ARG 3.4 6.5 - - - +
143B LEU* 4.1 12.8 - - + +
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Residues in contact with GLU 60 (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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58B THR* 3.8 1.7 + - + +
59B LEU* 1.3 70.7 - - - +
61B TRP* 1.3 60.4 + - - +
62B VAL* 3.3 18.2 + - + +
69B SER* 2.7 30.0 + - - -
70B VAL 5.5 0.2 - - - +
73B THR* 3.8 12.8 - - + -
92B ASN* 3.4 28.4 + - - +
94B THR 4.0 4.3 - - - +
96B MET* 3.2 26.2 + - - +
141B CYS* 3.3 4.3 - - - -
142B ARG* 2.9 61.9 + - + +
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Residues in contact with TRP 61 (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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32B PRO* 4.2 2.9 - - + -
44B LEU* 3.3 37.0 - - + -
45B LYS* 4.1 0.4 - - - -
46B CYS* 3.7 21.3 - - - -
59B LEU* 3.6 24.2 - - + +
60B GLU* 1.3 70.5 - - - +
62B VAL* 1.3 62.1 + - - +
63B VAL* 3.9 0.6 + - - -
69B SER* 3.4 3.8 - - - -
70B VAL* 3.1 44.6 + - + +
72B VAL 4.2 9.9 + - - -
73B THR* 5.0 0.8 - - - +
74B SER* 3.2 19.3 + - - -
76B TYR* 5.7 0.2 - - - -
113B VAL* 3.9 21.5 - - + +
123B GLY 3.3 20.6 - - - -
124B ASN* 4.2 0.7 - - - -
125B LEU* 3.6 27.4 - - + -
139B VAL* 3.6 18.6 - - + -
140B ARG 4.0 1.3 - - - -
141B CYS* 3.5 24.2 - - - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 3.8 34.1 - - - +
61B TRP* 1.3 70.8 - - - +
63B VAL* 1.3 62.0 + - - +
64B VAL* 3.5 10.7 + - + +
68B ASN 3.9 6.1 - - - +
69B SER* 4.1 4.9 - - - +
96B MET* 4.4 8.5 - - + -
97B HIS* 3.6 27.6 - - + +
139B VAL* 3.3 2.6 - - - -
140B ARG* 2.8 48.6 + - + +
142B ARG* 4.2 11.7 - - + -
174B TYR* 4.0 24.5 - - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP 3.9 0.9 + - - +
62B VAL* 1.3 71.7 - - - +
64B VAL* 1.3 63.5 + - - +
65B LYS 4.6 0.2 - - - +
66B LEU* 3.4 31.5 + - + +
67B GLN 3.1 14.0 + - - -
68B ASN 2.8 24.9 + - - +
70B VAL* 4.5 11.0 - - + -
105B LEU* 3.7 22.0 - - + -
111B PHE* 3.8 22.0 - - + -
135B SER* 3.8 26.7 - - - +
138B SER* 4.2 5.2 - - - +
139B VAL* 3.9 11.7 - - + +
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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