Contacts of the strand formed by residues 139 - 150 (chain B) in PDB entry 6CA0
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 SER 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B LYS* 4.9 7.6 + - - +
72B GLU 4.3 9.0 + - - +
74B VAL* 4.8 3.1 - - - +
104B LYS 3.8 2.2 - - - -
105B SER* 4.0 12.9 + - - -
133B LEU* 3.7 3.4 - - - +
137B ASN* 3.2 16.1 + - - -
138B ALA* 1.3 76.8 + - - +
140B ILE* 1.3 67.8 + - - +
141B SER* 4.2 1.2 + - - -
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Residues in contact with ILE 140 (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 ILE* 5.4 6.3 - - + -
71B LYS* 5.3 11.4 - - + +
74B VAL* 4.5 18.8 - - + -
81B ILE* 5.8 4.5 - - + -
102B LEU* 4.1 8.3 - - + +
103B ASN* 3.2 10.9 - - - +
104B LYS* 2.7 64.3 + - + +
110B VAL* 4.0 18.6 - - + -
131B CYS* 4.5 12.1 - - - -
133B LEU* 3.6 11.2 - - + +
139B SER* 1.3 80.1 - - - +
141B SER* 1.3 64.0 + - - +
142B MET* 3.9 25.8 - - + -
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Residues in contact with SER 141 (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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60B GLU 4.3 2.4 - - - +
61B ILE* 4.7 4.5 - - - +
62B ASP* 3.9 35.1 + - - +
71B LYS* 5.4 0.3 + - - -
101B THR* 5.6 1.0 + - - -
102B LEU 3.3 6.1 + - - -
103B ASN* 4.7 8.3 + - - +
139B SER* 4.2 1.3 + - - -
140B ILE* 1.3 80.1 - - - +
142B MET* 1.3 66.8 + - - +
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Residues in contact with MET 142 (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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59B VAL* 3.9 17.7 - - + -
60B GLU 3.2 16.6 - - - +
61B ILE* 3.8 20.6 - - + -
62B ASP* 5.5 0.4 - - - +
81B ILE* 5.5 10.1 - - + -
85B LEU* 4.4 14.1 - - + -
101B THR* 3.0 23.0 + - - -
102B LEU* 2.9 52.5 + - + +
130B ILE* 6.4 0.9 - - + -
140B ILE* 3.9 27.1 - - + -
141B SER* 1.3 76.6 + - - +
143B ARG* 1.3 70.3 + - - +
144B ILE* 4.3 5.6 - - + +
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Residues in contact with ARG 143 (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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59B VAL* 3.2 0.4 - - - -
60B GLU* 2.7 59.1 + - + +
99B ILE* 3.7 35.7 - - + -
100B LEU 3.3 5.4 - - - -
101B THR* 4.7 12.2 + - - +
142B MET* 1.3 81.5 - - - +
144B ILE* 1.3 58.2 + - - +
170B ARG* 3.1 10.8 + - - +
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Residues in contact with ILE 144 (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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56B VAL* 3.7 37.5 - - + -
58B GLU 3.4 11.0 - - - +
59B VAL* 3.9 12.1 - - + +
85B LEU* 4.2 20.2 - - + +
88B LEU* 6.3 3.4 - - + -
99B ILE* 4.3 1.8 - - - -
100B LEU* 2.4 74.5 + - + +
101B THR 5.2 0.2 - - - -
102B LEU* 4.8 19.5 - - + -
115B ILE* 5.6 8.7 - - + -
142B MET* 4.1 6.0 - - + -
143B ARG* 1.3 68.5 - - - +
145B LYS* 1.3 60.6 + - - +
146B VAL* 4.0 7.1 + - + +
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Residues in contact with LYS 145 (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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56B VAL* 3.6 4.0 - - - +
57B THR* 2.7 37.4 + - - +
58B GLU* 2.5 52.4 + - + +
97B GLU* 3.7 42.7 + - - +
98B VAL 3.3 17.7 - - - +
99B ILE* 4.0 4.5 - - + +
143B ARG 4.1 0.8 + - - -
144B ILE* 1.3 72.1 - - - +
146B VAL* 1.3 59.1 + - - +
147B GLN* 5.2 6.9 + - - -
170B ARG* 3.4 19.5 - - - +
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Residues in contact with VAL 146 (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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54B CYS* 5.7 0.2 - - + -
55B ALA 3.2 17.9 - - - +
56B VAL* 3.9 14.4 - - + +
57B THR* 4.1 0.2 - - - -
90B VAL* 4.1 24.9 - - + -
92B VAL* 4.2 16.8 - - + -
96B ASP 3.9 0.9 - - - +
97B GLU* 3.7 1.7 - - - -
98B VAL* 3.0 51.4 + - + +
100B LEU* 4.8 16.6 - - + -
144B ILE* 4.0 10.7 + - + +
145B LYS* 1.3 78.7 - - - +
147B GLN* 1.3 59.8 + - - +
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Residues in contact with GLN 147 (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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54B CYS* 3.3 4.3 - - - +
55B ALA 2.9 31.2 + - - -
57B THR* 3.2 28.9 + - - +
92B VAL* 6.4 0.2 - - - -
96B ASP* 3.3 9.3 + - - +
97B GLU* 3.4 36.7 + - + -
145B LYS* 5.2 4.3 + - - -
146B VAL* 1.3 74.3 - - - +
148B ARG* 1.3 74.9 + - - +
149B GLY* 5.9 0.4 - - - -
158B ARG* 3.9 12.0 + - - +
177B TYR* 3.1 21.9 + - - +
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Residues in contact with ARG 148 (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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52B PRO* 5.7 7.1 - - - +
53B GLY 3.3 6.7 + - - +
54B CYS* 3.6 21.7 - - - -
92B VAL* 4.5 7.6 + - + -
93B GLN 4.3 17.3 + - - -
94B GLY 4.6 4.9 + - - -
95B LYS 3.2 28.9 - - - +
96B ASP* 2.9 40.3 + - - +
147B GLN* 1.3 86.8 + - - +
149B GLY* 1.3 57.5 + - - +
150B ARG* 5.4 11.7 + - - +
177B TYR* 3.6 1.1 - - - -
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Residues in contact with GLY 149 (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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53B GLY 2.6 44.5 + - - +
148B ARG* 1.3 75.4 - - - +
150B ARG* 1.3 70.3 + - - -
177B TYR* 3.2 26.0 - - - +
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Residues in contact with ARG 150 (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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7A GLU* 3.7 55.5 + - - +
8A PHE* 3.5 31.3 - - + -
195A ARG* 5.7 1.0 - - - +
49B SER 4.7 1.6 - - - +
50B SER* 5.1 1.1 - - - -
51B MET 3.3 4.5 - - - +
52B PRO* 3.6 20.6 - - + -
148B ARG* 5.4 11.3 + - - +
149B GLY* 1.3 82.9 - - - +
151B GLY* 1.3 63.0 + - - +
152B TYR 4.0 0.3 + - - -
153B VAL* 4.8 9.5 - - - +
177B TYR* 4.3 3.4 - - - -
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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