Contacts of the strand formed by residues 117 - 123 (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 GLU 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 4.0 10.0 - - + +
81A ALA 5.4 0.9 + - - -
82A ARG* 2.9 43.8 + - - +
95A LYS* 5.3 0.2 + - - -
96A GLY 3.3 3.6 - - - -
98A TYR* 2.7 41.7 + - + +
113A THR* 3.3 21.1 + - - -
114A ALA* 3.1 26.9 + - + +
115A GLU 3.3 3.0 - - - +
116A ASN* 1.3 94.8 - - - +
118A ILE* 1.3 72.6 + - - +
119A PHE* 3.7 6.4 - - + -
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Residues in contact with ILE 118 (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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95A LYS* 3.9 32.3 - - + +
96A GLY 2.9 9.2 + - - +
97A VAL* 3.3 10.4 - - + -
98A TYR* 2.9 26.7 + - - +
113A THR* 4.9 0.7 - - - -
117A GLU* 1.3 81.7 - - - +
119A PHE* 1.3 73.1 + - - +
120A VAL* 4.2 5.6 - - + +
131A ILE* 5.0 13.5 - - + -
132A THR* 6.1 0.7 - - - -
135A TYR* 3.8 50.7 - - + -
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Residues in contact with PHE 119 (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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82A ARG* 5.0 9.4 - - + -
84A ASN* 6.0 1.3 - - - -
98A TYR* 3.4 47.3 - + + -
100A LYS* 4.4 28.9 - - + -
110A ASP* 4.5 5.5 - - - +
112A GLN 5.6 0.7 - - - -
113A THR* 2.7 43.1 + - + +
117A GLU* 3.7 14.6 - - + -
118A ILE* 1.3 79.6 - - - +
120A VAL* 1.3 63.7 + - - +
121A ARG* 3.4 38.1 + - + +
131A ILE* 4.8 9.0 - - - +
132A THR* 3.6 6.6 + - - -
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Residues in contact with VAL 120 (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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42A VAL* 4.8 2.5 - - + -
46A ILE* 4.2 23.1 - - + -
97A VAL* 3.8 21.5 - - + -
98A TYR 2.8 12.8 + - - +
99A VAL* 3.4 15.8 - - + -
100A LYS* 2.8 31.5 + - - +
118A ILE* 3.8 2.6 + - + -
119A PHE* 1.3 70.9 - - - +
121A ARG* 1.3 58.6 + - - +
122A VAL* 4.0 13.9 - - + -
132A THR* 3.5 24.2 - - + +
135A TYR* 4.1 24.2 - - + -
136A LEU* 4.5 4.9 - - + -
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Residues in contact with ARG 121 (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* 3.5 21.9 - - + +
102A TYR* 2.7 36.8 + - + +
108A PRO* 3.7 12.3 - - + +
109A THR 3.4 22.0 + - - -
110A ASP* 3.9 11.5 + - - +
111A TYR* 3.3 51.0 + - - +
112A GLN 5.8 0.2 + - - -
113A THR* 5.8 0.8 - - - +
119A PHE* 3.9 39.5 - - + +
120A VAL* 1.3 77.1 - - - +
122A VAL* 1.3 63.4 + - - +
129A SER* 3.0 32.2 + - - +
132A THR* 2.9 10.6 + - - -
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Residues in contact with VAL 122 (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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42A VAL* 4.7 11.4 - - + -
99A VAL* 5.2 1.1 - - + -
100A LYS 3.0 13.9 + - - +
101A VAL* 3.3 17.0 - - + -
102A TYR* 2.8 24.5 + - - -
108A PRO* 4.0 5.6 - - - +
120A VAL* 4.0 19.7 - - + -
121A ARG* 1.3 79.5 - - - +
123A SER* 1.3 58.8 + - - +
127A GLN 3.2 11.2 - - - +
128A MET* 4.1 16.4 - - + -
132A THR* 4.2 2.7 - - + -
136A LEU* 5.6 0.7 - - + -
144A VAL* 4.4 14.4 - - + -
148A LEU* 3.8 25.6 - - + -
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Residues in contact with SER 123 (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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101A VAL* 4.9 3.1 - - - -
102A TYR* 3.3 7.0 - - - -
104A ASP* 3.4 21.1 - - - -
106A GLY 3.4 19.9 + - - -
108A PRO* 4.1 1.9 - - - +
122A VAL* 1.3 73.4 - - - +
124A LEU* 1.3 65.4 + - - +
125A SER* 3.0 20.1 + - - -
126A GLY 2.9 11.1 + - - -
127A GLN* 2.9 29.3 + - - +
148A LEU* 3.6 14.7 - - - +
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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