Contacts of the strand formed by residues 117 - 123 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 5.2 0.3 - - - +
80B PHE* 4.1 9.9 - - + +
81B ALA 5.4 0.7 + - - -
82B ARG* 2.9 42.1 + - - +
95B LYS* 4.5 0.7 + - - +
96B GLY 3.3 4.0 - - - -
98B TYR* 2.7 39.9 + - + +
113B THR* 3.4 24.3 + - - -
114B ALA* 3.1 27.4 + - + +
115B GLU 3.3 2.6 - - - +
116B ASN* 1.3 92.7 - - - +
118B ILE* 1.3 72.6 + - - +
119B PHE* 3.9 3.9 - - + -
1169B GOL 4.7 1.8 + - - -
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Residues in contact with ILE 118 (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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95B LYS* 3.3 39.3 - - + +
96B GLY 2.9 8.8 + - - +
97B VAL* 3.3 9.0 - - + -
98B TYR* 2.9 27.9 + - - +
113B THR* 4.9 0.7 - - - -
117B GLU* 1.3 74.5 - - - +
119B PHE* 1.3 74.3 + - - +
120B VAL* 4.2 5.6 - - + +
131B ILE* 5.0 13.7 - - + -
132B THR* 6.1 0.7 - - - -
135B TYR* 3.8 52.9 - - + -
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Residues in contact with PHE 119 (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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68A VAL* 6.5 0.9 - - + -
1168A GOL 6.1 2.5 - - - -
82B ARG* 5.3 7.4 - - + -
98B TYR* 3.5 34.1 - + + -
100B LYS* 2.9 44.0 - - + -
110B ASP* 4.6 5.0 - - - +
112B GLN 5.8 0.2 - - - -
113B THR* 2.7 41.7 + - + +
117B GLU* 3.9 11.7 - - + -
118B ILE* 1.3 81.5 - - - +
120B VAL* 1.3 63.7 + - - +
121B ARG* 3.5 37.1 + - + +
131B ILE* 4.7 9.5 - - - +
132B THR* 3.6 7.1 + - - -
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Residues in contact with VAL 120 (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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42B VAL* 4.7 3.4 - - + -
46B ILE* 4.3 21.8 - - + -
97B VAL* 3.8 21.3 - - + -
98B TYR 2.8 12.9 + - - +
99B VAL* 3.5 15.2 - - + -
100B LYS* 2.9 28.2 + - - +
118B ILE* 3.9 2.4 + - + -
119B PHE* 1.3 69.8 - - - +
121B ARG* 1.3 60.5 + - - +
122B VAL* 4.0 13.7 - - + -
132B THR* 3.6 21.8 - - + +
135B TYR* 4.0 24.2 - - + -
136B LEU* 4.5 7.9 - - + -
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Residues in contact with ARG 121 (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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68A VAL* 3.6 29.5 - - - +
71A GLN* 5.2 0.2 + - - -
100B LYS* 3.6 15.9 - - + +
102B TYR* 2.7 39.7 + - + -
108B PRO* 3.8 12.2 - - + +
109B THR 3.3 21.8 + - - -
110B ASP* 3.9 11.8 + - - +
111B TYR* 3.4 35.3 + - - +
112B GLN 5.7 0.8 + - - -
113B THR* 4.8 1.0 - - - +
119B PHE* 3.7 40.8 - - + +
120B VAL* 1.3 77.8 - - - +
122B VAL* 1.3 62.4 + - - +
128B MET* 3.6 0.2 - - - -
129B SER* 3.0 36.3 + - - +
132B THR* 2.9 9.8 + - - -
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Residues in contact with VAL 122 (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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42B VAL* 4.6 11.7 - - + -
99B VAL* 5.1 1.1 - - + -
100B LYS 3.1 10.8 + - - +
101B VAL* 3.3 18.2 - - + -
102B TYR* 2.8 23.8 + - - +
108B PRO* 4.0 5.1 - - - +
120B VAL* 4.0 19.3 - - + -
121B ARG* 1.3 79.9 - - - +
123B SER* 1.3 58.3 + - - +
127B GLN 3.1 10.5 - - - +
128B MET* 4.1 17.3 - - + -
132B THR* 4.1 2.5 - - + -
136B LEU* 5.6 0.2 - - + -
144B VAL* 4.3 13.0 - - + -
148B LEU* 3.8 25.6 - - + -
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Residues in contact with SER 123 (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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101B VAL* 4.9 2.5 - - - -
102B TYR* 3.5 7.2 - - - -
103B PRO 3.3 17.3 - - - -
106B GLY 3.7 11.2 - - - -
108B PRO* 4.1 2.8 - - - +
122B VAL* 1.3 74.1 - - - +
124B LEU* 1.3 66.1 + - - +
125B SER* 3.2 8.1 + - - -
126B GLY 2.9 11.3 + - - -
127B GLN* 2.8 51.9 + - - -
148B LEU* 3.6 13.5 - - - +
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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