Contacts of the strand formed by residues 112 - 124 (chain E) in PDB entry 4IHB
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 PRO 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104E PRO* 5.3 2.9 - - + -
105E LEU 3.4 9.6 - - - +
106E LEU* 3.7 11.9 - - + -
107E ASP* 4.8 1.0 - - - +
110E LYS 4.1 1.1 - - - +
111E GLN* 1.3 86.2 + - - +
113E THR* 1.3 63.6 + - - +
114E GLY 4.4 4.0 - - - +
0F PHE* 6.1 1.6 - - - -
59F LEU* 4.1 8.3 - - + -
92F LEU* 4.3 7.0 - - + -
97F LEU* 3.8 34.1 - - + -
123F TYR* 3.6 50.4 + - + -
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Residues in contact with THR 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LEU 3.5 22.3 + - - +
82E GLY* 4.4 0.9 - - - -
105E LEU* 2.9 25.4 + - - +
106E LEU 3.8 2.2 - - - +
107E ASP* 3.6 30.7 - - + +
112E PRO* 1.3 73.0 - - - +
114E GLY* 1.3 55.7 + - - +
115E ALA* 3.0 25.3 + - - +
205E FMT 3.5 27.7 + - - -
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Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASN* 3.7 23.0 + - - +
105E LEU 4.5 0.2 + - - -
112E PRO* 3.2 8.2 - - - +
113E THR* 1.3 78.8 - - - +
115E ALA* 1.3 61.3 + - - +
116E SER* 5.4 0.3 - - - -
205E FMT 4.7 0.2 - - - -
95F PRO* 6.1 1.0 - - - +
97F LEU* 5.7 5.8 - - - -
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLU 3.2 10.3 - - - +
11E ASN 3.2 20.4 + - - +
12E VAL* 4.1 5.4 - - + -
104E PRO* 3.6 4.2 - - - +
105E LEU* 2.9 39.6 + - + +
113E THR* 3.0 16.1 + - - +
114E GLY* 1.3 82.0 + - - +
116E SER* 1.3 62.9 + - - +
205E FMT 3.7 11.7 - - - +
95F PRO* 5.8 0.6 - - - +
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Residues in contact with SER 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 3.1 7.3 - - - +
10E GLU* 2.9 48.0 + - - +
11E ASN* 5.5 1.4 + - - -
102E ASN* 3.6 10.2 + - - -
103E ALA 3.2 12.3 - - - -
104E PRO* 4.2 0.4 - - - -
105E LEU* 4.1 4.7 - - - +
114E GLY 4.2 1.0 + - - -
115E ALA* 1.3 76.9 - - - +
117E LEU* 1.3 62.1 + - - +
118E VAL* 5.4 1.5 - - - +
95F PRO* 3.5 32.9 - - - +
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Residues in contact with LEU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.1 13.5 - - + -
8E TYR 3.4 15.9 - - - +
9E ALA* 4.2 3.8 - - + -
24E CYS* 4.2 5.2 - - - -
46E TRP* 3.6 24.9 - - + -
67E VAL* 3.3 35.2 - - + -
69E VAL* 4.6 3.8 - - + -
84E ALA* 5.0 4.0 - - + -
101E PHE 3.3 2.9 - - - +
103E ALA* 2.7 39.6 + - + +
105E LEU* 3.8 23.1 - - + -
116E SER* 1.3 74.7 - - - +
118E VAL* 1.3 64.6 + - - +
119E LEU* 3.7 25.5 - - + +
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Residues in contact with VAL 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.2 0.3 - - - -
7E LEU* 3.1 38.3 + - + -
8E TYR* 2.8 63.4 + - + +
10E GLU* 5.7 0.4 - - + +
100E SER* 6.2 2.0 - - - -
101E PHE 3.3 7.4 - - - +
102E ASN* 3.3 33.7 - - + +
116E SER* 5.4 1.8 - - - +
117E LEU* 1.3 73.3 - - - +
119E LEU* 1.3 67.9 + - - +
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Residues in contact with LEU 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E VAL* 4.3 5.4 - - + -
5E PHE 3.2 16.2 - - - +
6E ILE* 4.3 8.5 - - + -
7E LEU* 4.5 2.9 - - - +
65E LEU* 4.1 18.2 - - + -
67E VAL* 4.6 11.0 - - + -
86E VAL* 4.4 15.5 - - + -
100E SER* 3.4 3.4 - - - -
101E PHE* 2.7 57.3 + - + +
103E ALA* 4.8 4.5 - - + -
117E LEU* 3.7 35.7 - - + +
118E VAL* 1.3 79.0 - - - +
120E GLN* 1.3 57.7 + - - +
121E VAL* 4.0 21.5 - - + -
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Residues in contact with GLN 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ARG* 4.3 2.3 + - - +
4E VAL* 3.4 3.6 - - - +
5E PHE* 2.8 68.3 + - + +
7E LEU* 5.0 8.9 - - + +
98E SER* 4.3 12.1 - - - -
99E ALA 3.5 14.2 + - - +
100E SER* 4.3 10.2 - - - -
119E LEU* 1.3 74.6 - - - +
121E VAL* 1.3 74.8 + - - +
122E SER* 3.8 18.0 + - - -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 3.6 27.4 - - + -
3E ARG 3.3 3.6 - - - -
4E VAL* 4.0 17.9 - - + -
65E LEU* 4.2 5.8 - - + -
86E VAL* 4.8 3.1 - - + -
88E LEU* 4.6 7.4 - - + -
91E VAL* 3.9 21.5 - - + +
98E SER* 3.2 3.8 - - - -
99E ALA 2.9 34.3 + - - +
101E PHE* 4.1 13.9 - - + -
119E LEU* 4.0 23.1 - - + -
120E GLN* 1.3 84.0 + - - +
122E SER* 1.3 65.6 + - - +
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Residues in contact with SER 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 3.3 1.2 - - - +
2E LEU* 3.4 7.2 - - - +
3E ARG* 2.8 66.5 + - - +
91E VAL* 4.1 2.0 - - - -
97E LEU 3.2 14.1 - - - -
98E SER* 3.5 4.9 - - - -
120E GLN* 3.8 7.6 + - - -
121E VAL* 1.3 78.3 - - - +
123E TYR* 1.3 66.2 + - - +
201E FMT 3.4 19.7 - - - -
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Residues in contact with TYR 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.9 23.1 - - + -
0E PHE* 4.1 11.8 - - + -
1E MET 3.1 5.8 - - - +
2E LEU* 4.0 20.4 - - + -
28E PHE* 5.9 0.4 - + - -
54E LEU* 3.7 31.0 - - + -
59E LEU* 3.5 25.6 - - + +
88E LEU* 3.3 32.4 + - + +
91E VAL* 3.5 28.5 - - + -
92E LEU* 3.5 29.5 - - + +
97E LEU* 2.9 29.3 + - + +
122E SER* 1.3 73.4 - - - +
124E THR* 1.3 59.6 + - - +
201E FMT 3.8 13.5 + - - -
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Residues in contact with THR 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0E PHE* 3.4 10.2 - - - -
1E MET* 2.7 51.9 + - + +
3E ARG* 3.4 49.5 + - + +
51E GLU* 4.0 10.5 - - - +
122E SER* 4.5 0.2 - - - -
123E TYR* 1.3 75.4 - - - +
125E ALA* 1.3 72.2 + - - +
201E FMT 4.6 3.9 + - - -
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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