Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 4CGS
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 LYS 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.3 2.6 - - - +
80A PHE* 4.0 5.8 - - - -
89A LEU* 3.7 3.3 - - - +
90A ASP* 2.8 40.0 + - + +
93A GLU* 3.6 32.5 - - + +
94A ARG* 1.3 82.1 + - - +
96A GLY* 1.3 59.4 + - - +
97A VAL* 4.9 0.7 - - + -
115A GLU 2.5 25.2 + - - +
116A ASN* 3.2 20.8 - - - +
117A GLU 4.2 0.6 + - - +
118A ILE* 3.9 35.8 - - + +
135A TYR* 5.4 0.2 - - + -
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.3 25.1 - - - -
86A PRO* 3.8 10.5 - - - -
88A LEU 3.6 7.2 - - - -
89A LEU* 4.5 1.1 - - - -
95A LYS* 1.3 73.2 - - - +
97A VAL* 1.3 60.3 + - - -
98A TYR* 4.1 2.6 - - - -
116A ASN 2.8 9.9 + - - -
117A GLU* 3.3 6.4 - - - +
118A ILE 2.9 25.8 + - - +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 5.0 3.1 - - + -
58A TYR* 4.4 5.6 - - + -
86A PRO* 3.7 0.2 - - - +
87A ASP* 2.9 26.6 + - - +
88A LEU* 2.8 42.1 + - + +
90A ASP* 4.1 16.6 - - + -
95A LYS* 4.4 1.3 - - + +
96A GLY* 1.3 77.3 - - - +
98A TYR* 1.3 66.9 + - - +
99A VAL* 4.5 0.7 - - + -
118A ILE* 3.3 13.7 - - + +
120A VAL* 3.8 29.2 - - + -
135A TYR* 3.6 28.5 - - + +
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 4.1 6.8 - - - +
82A ARG* 3.4 15.1 - - + +
84A ASN* 3.8 32.5 - - - -
85A VAL 4.1 2.0 - - - -
86A PRO* 3.6 42.0 - - + +
87A ASP* 3.5 9.9 - - - +
96A GLY 4.1 5.8 - - - -
97A VAL* 1.3 75.4 - - - +
99A VAL* 1.3 59.9 + - - +
100A LYS* 5.3 3.4 - - + -
117A GLU* 2.7 45.6 + - + +
118A ILE 2.9 10.9 + - - -
119A PHE* 3.4 41.0 - + + +
120A VAL* 2.8 32.6 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 3.3 46.1 + - + +
42A VAL* 3.8 23.8 - - + -
43A CYS* 3.9 20.6 - - - -
46A ILE* 4.1 15.9 - - + -
87A ASP* 2.9 11.8 + - + +
88A LEU* 3.9 15.9 - - + -
97A VAL* 4.5 0.7 - - + -
98A TYR* 1.3 78.4 - - - +
100A LYS* 1.3 74.2 + - - +
101A VAL* 4.3 4.3 - - + -
120A VAL* 3.4 13.9 - - + +
122A VAL* 5.2 1.1 - - + -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 5.6 0.4 - - - -
98A TYR* 5.3 2.2 - - + -
99A VAL* 1.3 80.1 - - - +
101A VAL* 1.3 62.4 + - - +
102A TYR* 3.6 29.7 - - + +
119A PHE* 4.4 28.6 - - + -
120A VAL 2.8 13.2 + - - +
121A ARG* 3.5 18.7 - - + +
122A VAL* 3.0 29.1 + - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.2 19.8 - - + +
38A ILE* 4.2 14.8 - - + +
39A LYS* 3.9 38.2 - - + +
42A VAL* 5.0 1.1 - - + -
99A VAL* 4.6 4.5 - - + -
100A LYS* 1.3 75.3 - - - +
102A TYR* 1.3 64.6 + - - +
103A PRO* 3.4 11.3 - - - +
122A VAL* 3.3 19.5 - - + +
123A SER 4.9 0.7 - - - -
124A LEU* 3.5 35.4 - - + +
148A LEU* 5.0 0.4 - - + -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 3.6 25.8 - - + +
101A VAL* 1.3 73.5 - - - +
103A PRO* 1.4 66.2 - - - +
104A ASP* 3.1 25.6 - - + +
108A PRO* 3.7 19.7 - - + -
109A THR 4.5 3.3 + - - -
111A TYR* 5.9 0.9 - - - -
121A ARG* 2.7 55.3 + - + +
122A VAL 2.8 20.6 + - - +
123A SER* 4.1 0.9 - - - -
124A LEU* 2.8 26.9 + - - -
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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