Contacts of the strand formed by residues 103 - 112 (chain J) in PDB entry 3IT8
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 LEU 103 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98J TYR* 4.0 11.4 - - + +
99J GLU* 3.5 2.6 - - - +
100J THR* 3.0 31.4 + - - +
101J GLY 3.7 1.2 - - - +
102J LEU* 1.3 79.9 - - + +
104J PHE* 1.3 65.9 + - - +
213J ILE* 3.5 39.7 - - + -
215J LYS* 4.2 21.8 - - - +
228J TYR* 5.0 3.4 - - + +
284J PHE* 3.5 44.0 - - + -
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Residues in contact with PHE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ASN* 3.8 23.1 - - - -
31G ARG* 3.2 49.4 - - + +
32G ARG 4.8 4.5 - - - -
98J TYR* 3.2 24.6 + - - +
99J GLU* 4.1 8.5 - - + -
102J LEU 3.4 11.7 - - - -
103J LEU* 1.3 77.2 - - - +
105J GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J CYS* 3.2 4.9 - - - +
98J TYR* 3.0 50.0 + - - +
104J PHE* 1.3 79.3 - - - +
106J SER* 1.3 60.2 + - - -
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Residues in contact with SER 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J GLY 3.3 13.2 - - - -
97J CYS* 3.9 9.4 - - - +
98J TYR* 4.1 1.5 - - - -
105J GLY* 1.3 75.4 - - - -
107J TYR* 1.3 67.6 + - - +
159J GLU* 2.6 44.2 + - - +
163J CYS* 5.2 2.7 - - - -
164J SER* 5.9 3.6 - - - -
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Residues in contact with TYR 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 5.5 1.9 - - - +
3J LEU 3.5 16.5 + - - -
4J LYS* 3.6 18.5 - - - +
94J ILE* 3.8 11.7 - - + -
95J THR* 2.8 29.6 + - - -
96J GLY* 2.8 46.2 + - - +
97J CYS* 3.8 10.5 + - - -
98J TYR* 4.5 4.9 - + + -
106J SER* 1.3 80.4 - - - +
108J GLY* 1.3 59.0 + - - +
109J TYR* 4.0 6.3 - + + -
159J GLU* 3.5 14.7 - - - +
246J GLY 3.5 26.5 - - - -
247J GLU* 4.0 28.7 - - + +
248J PRO* 3.3 23.6 - - + +
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Residues in contact with GLY 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J ILE 3.2 8.3 - - - -
95J THR* 3.8 8.7 - - - -
107J TYR* 1.3 78.7 - - - +
109J TYR* 1.3 61.7 + - - +
119J ARG* 3.9 3.4 - - - +
120J TYR* 2.8 34.5 + - - +
155J LEU* 4.1 10.1 - - - -
159J GLU* 3.4 14.7 + - - +
247J GLU* 5.4 0.2 + - - -
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Residues in contact with TYR 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J SER 3.9 0.2 - - - +
93J LEU* 3.7 5.2 - - - +
94J ILE* 2.8 61.7 + - + +
107J TYR* 4.0 9.2 - + - -
108J GLY* 1.3 77.0 - - - +
110J VAL* 1.3 69.0 + - - +
111J GLU* 3.3 25.2 + - + -
118J ALA 3.2 14.4 - - - +
119J ARG* 3.8 9.0 - - + -
120J TYR 4.5 0.2 - - - +
127J PHE* 4.9 2.0 - - - -
130J MET* 3.6 23.6 - - + -
243J TYR* 3.7 11.8 - + - -
247J GLU* 3.7 35.7 - - + -
248J PRO* 3.4 10.1 - - + +
249J GLY* 3.2 26.9 + - - -
325J NAG 4.6 1.7 - - - +
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Residues in contact with VAL 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU* 3.5 33.4 - - + -
92J SER 3.3 8.3 - - - +
93J LEU* 3.9 19.7 - - + -
109J TYR* 1.3 75.3 - - - +
111J GLU* 1.3 61.5 + - - +
117J LEU* 2.9 36.9 + - + +
118J ALA 2.7 16.4 + - - +
127J PHE* 4.0 17.5 - - + -
130J MET* 3.2 3.4 - - - +
140J MET* 4.0 19.7 - - + -
141J LEU* 4.3 13.5 - - + -
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Residues in contact with GLU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J LEU* 3.4 7.5 - - - +
92J SER* 2.9 46.8 + - - -
94J ILE* 4.0 16.3 - - + +
109J TYR* 3.3 18.9 + - + -
110J VAL* 1.3 75.5 - - - +
112J THR* 1.3 64.4 + - - +
115J GLY* 3.9 5.8 - - - +
116J PRO* 3.9 16.6 - - + -
117J LEU* 3.9 2.0 - - - +
243J TYR* 3.1 19.9 + - - -
249J GLY* 5.4 1.0 - - - -
325J NAG 3.9 24.5 + - - +
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Residues in contact with THR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J LEU* 6.1 0.2 - - - +
80J ILE* 4.7 5.2 - - - +
86J THR* 5.9 1.6 - - + +
88J THR* 3.3 14.3 + - + +
90J SER* 3.8 8.4 + - - -
91J LEU* 3.7 17.5 - - - +
111J GLU* 1.3 78.3 - - - +
113J ALA* 1.3 59.8 + - - +
114J ASN* 2.8 45.3 - - + +
115J GLY* 2.8 28.6 + - - +
117J LEU* 4.1 16.7 - - + +
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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