Contacts of the strand formed by residues 77 - 86 (chain C) in PDB entry 6CNB
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 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C PRO* 1.3 82.0 + - - +
78C VAL* 1.3 60.1 + - - +
110C PRO* 5.2 5.8 - - - -
210C LEU* 3.1 9.5 - - - +
211C GLY* 2.7 39.5 + - - +
212C ILE* 4.9 0.2 - - - +
219C PHE* 3.2 25.4 + - - -
221C PRO* 3.0 31.3 - - - +
307C ALA* 5.3 7.2 - - - -
308C MET* 4.9 2.8 - - - +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C SER* 1.3 81.6 - - - +
79C ALA* 1.3 63.2 + - - +
105C PRO* 5.8 0.2 - - - +
106C LEU* 4.3 17.0 + - + +
108C VAL* 3.4 36.6 - - + +
110C PRO* 5.1 9.6 - - + -
113C LEU* 4.6 5.6 - - + -
132C ILE* 3.9 21.3 - - + -
208C CYS* 3.5 17.5 - - - -
209C ILE 3.1 21.5 - - - +
210C LEU* 4.2 10.8 - - + -
307C ALA* 6.4 1.8 - - + -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL* 1.3 76.5 - - - +
80C ALA* 1.3 66.8 + - - +
81C GLU* 3.3 3.1 + - - +
102C GLY 4.0 11.4 - - - +
103C LEU 5.1 0.4 - - - +
104C VAL 4.7 7.6 - - - +
105C PRO* 5.7 2.7 - - + -
106C LEU* 4.4 4.3 - - - -
208C CYS* 3.2 11.6 - - - -
209C ILE 3.3 14.2 + - - +
218C LYS 3.3 26.0 - - - +
219C PHE* 3.7 24.9 - - + -
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 1.3 72.9 - - - +
81C GLU* 1.3 59.8 + - - +
83C VAL* 5.7 0.9 - - + -
101C ILE* 3.6 37.8 + - + +
102C GLY* 3.2 25.1 + - - +
104C VAL* 5.1 2.3 + - + +
106C LEU* 4.2 8.3 - - + +
134C LEU* 5.2 6.7 - - + -
206C ALA* 4.8 7.0 - - + +
207C HIS 4.4 2.9 - - - +
208C CYS* 3.3 21.9 - - + -
218C LYS* 3.7 5.4 + - - -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA 3.3 2.6 + - - +
80C ALA* 1.3 75.4 - - - +
82C TYR* 1.3 96.3 + - + +
83C VAL* 3.7 2.2 + - - +
207C HIS 3.2 8.8 + - - +
208C CYS* 4.2 0.4 - - - +
209C ILE* 3.1 31.6 - - + +
218C LYS* 4.0 7.9 - - - +
219C PHE* 4.6 7.7 - - - -
68L GLU* 5.1 0.9 - - + -
69L ALA* 2.8 47.2 + - - +
70L ARG* 2.5 42.4 + - - -
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Residues in contact with TYR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLU* 1.3 113.0 + - + +
83C VAL* 1.3 59.6 + - - +
84C TYR* 4.9 10.5 - - + +
125C LYS* 4.6 12.6 + - - -
126C PHE* 3.5 37.6 - + + -
206C ALA* 3.2 6.2 - - - +
207C HIS* 2.9 43.5 + - + +
209C ILE* 5.5 4.5 - - + -
66L GLN* 3.6 26.5 - - - -
67L PHE 3.7 4.0 - - - +
68L GLU* 4.1 29.1 + - + +
70L ARG* 5.3 1.4 + - - -
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ALA* 5.7 0.4 - - + -
81C GLU 3.9 10.5 - - - +
82C TYR* 1.3 81.3 - - - +
84C TYR* 1.3 71.5 + - - +
85C PHE* 3.6 37.2 + - + -
98C ALA* 4.0 31.2 - - + +
101C ILE* 4.8 9.0 - - + -
102C GLY 5.3 0.4 - - - +
204C LEU* 4.3 13.7 - - + -
206C ALA* 3.6 14.1 - - + +
65L VAL 4.0 0.2 - - - +
66L GLN* 3.7 0.7 - - - -
67L PHE* 3.0 34.0 + - + +
69L ALA* 4.5 2.0 - - + -
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C TYR* 4.9 7.8 - - + +
83C VAL* 1.3 84.0 - - - +
85C PHE* 1.3 63.3 + - - +
86C PHE* 3.7 2.4 + - + -
126C PHE* 4.7 12.1 - - - -
204C LEU* 3.0 5.2 - - - +
205C LYS* 2.9 64.5 + - + +
207C HIS* 3.2 41.2 + + - -
64L LEU* 4.5 25.4 - - + -
65L VAL 3.8 3.6 - - - +
66L GLN* 3.4 49.8 + - + -
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 3.6 11.8 - - + -
84C TYR* 1.3 72.9 - - - +
86C PHE* 1.3 68.8 + - - +
87C ASN 3.2 20.5 + - - +
88C ASN* 4.7 8.7 - - + -
94C ASP* 2.5 46.9 - - + -
97C LEU* 4.2 7.4 - - + -
98C ALA* 3.7 24.5 - - + -
202C ILE* 5.6 0.2 - - + -
203C SER 3.8 1.1 - - - -
204C LEU* 3.4 38.1 - - + -
60L ARG* 5.5 0.9 - - - +
63L ARG 4.6 0.3 - - - +
64L LEU* 3.9 4.5 - - - +
65L VAL* 3.2 44.8 + - + +
67L PHE* 3.6 17.0 - + - -
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Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 3.7 5.5 + - + -
85C PHE* 1.3 76.5 - - - +
87C ASN* 1.3 80.2 + - - +
203C SER* 2.5 49.6 + - - +
204C LEU 5.3 1.6 - - - -
205C LYS* 3.5 42.8 - - + -
62L LYS 5.7 3.4 - - - -
64L LEU* 3.4 34.8 - - + +
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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