Contacts of the strand formed by residues 112 - 124 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B PHE* 3.1 34.5 - - + -
54B LEU* 5.9 0.7 - - + -
59B LEU* 3.8 17.3 - - + -
92B LEU* 4.2 20.0 - - + -
97B LEU* 3.7 33.7 - - + -
123B TYR* 4.5 9.2 - - + -
104C PRO* 5.5 2.5 - - + -
105C LEU 3.7 7.4 - - - +
106C LEU* 3.7 7.2 - - + -
107C ASP* 4.9 1.6 - - - +
111C GLN* 1.3 95.3 - - + +
113C THR* 1.3 60.2 + - - +
114C GLY 3.4 2.7 - - - +
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B PHE* 5.6 4.6 - - - -
11C ASN 5.3 1.2 - - - +
81C LEU 3.6 23.1 + - - +
105C LEU* 3.0 18.3 + - - +
106C LEU 3.8 1.6 - - - +
107C ASP* 3.6 37.5 - - + +
112C PRO* 1.3 72.6 - - - +
114C GLY* 1.3 58.8 + - - +
115C ALA* 3.2 24.9 + - - +
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B PHE* 5.7 0.6 - - - -
97B LEU* 5.7 6.3 - - - -
11C ASN* 3.6 23.6 - - - +
112C PRO* 3.4 6.4 - - - +
113C THR* 1.3 78.3 - - - +
115C ALA* 1.3 62.7 + - - +
116C SER* 5.3 0.5 - - - -
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLU 3.2 10.5 - - - +
11C ASN 3.3 19.2 + - - +
12C VAL* 4.4 8.7 - - + -
13C HIS 5.5 0.4 - - - +
81C LEU 5.9 0.9 - - - +
104C PRO* 3.6 4.7 - - - +
105C LEU* 3.0 37.5 + - + +
113C THR* 3.2 17.2 + - - +
114C GLY* 1.3 82.9 + - - +
116C SER* 1.3 63.2 + - - +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PRO* 3.7 22.9 - - - +
9C ALA* 3.2 6.9 - - - +
10C GLU* 2.9 51.8 + - - +
11C ASN* 5.1 1.4 + - - -
102C ASN* 3.4 19.5 + - - -
103C ALA 3.2 10.8 - - - -
104C PRO* 4.3 0.9 - - - -
105C LEU* 4.1 5.1 - - - +
114C GLY 5.3 0.7 - - - -
115C ALA* 1.3 77.1 - - - +
117C LEU* 1.3 61.4 + - - +
118C VAL* 4.3 1.7 - - - +
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.0 10.5 - - + -
8C TYR 3.5 15.5 - - - +
9C ALA* 4.1 3.8 - - + -
24C CYS* 3.9 9.9 - - - -
46C TRP* 3.7 24.2 - - + -
67C VAL* 3.4 34.3 - - + -
69C VAL* 4.6 2.2 - - + -
84C ALA* 5.1 3.8 - - + -
101C PHE 3.4 3.1 - - - +
102C ASN* 4.2 0.2 - - - -
103C ALA* 2.7 38.9 + - + +
105C LEU* 3.9 24.0 - - + +
116C SER* 1.3 76.6 - - - +
118C VAL* 1.3 62.7 + - - +
119C LEU* 3.8 28.2 - - + +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.0 0.7 - - - -
7C LEU* 3.0 44.8 + - + -
8C TYR* 2.8 60.2 + - + +
10C GLU* 5.8 0.2 - - - +
100C SER* 6.5 0.7 - - - -
101C PHE 3.3 7.6 - - - +
102C ASN* 3.5 32.5 - - + +
116C SER* 5.4 1.8 - - - +
117C LEU* 1.3 73.6 - - - +
119C LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C VAL* 4.2 6.7 - - + -
5C PHE 3.2 15.5 - - - +
6C ILE* 4.2 9.9 - - + -
7C LEU* 4.4 3.4 - - - +
65C LEU* 3.8 28.5 - - + -
67C VAL* 4.3 10.3 - - + -
84C ALA* 6.0 0.7 - - + -
86C VAL* 4.2 14.8 - - + -
100C SER* 3.5 1.4 - - - -
101C PHE* 2.7 55.9 + - + +
103C ALA* 4.9 4.3 - - + -
117C LEU* 3.8 34.3 - - + +
118C VAL* 1.3 78.3 - - - +
120C GLN* 1.3 58.2 + - - +
121C VAL* 4.1 12.3 - - + -
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ARG* 4.3 1.4 + - - +
4C VAL* 3.4 2.8 - - - +
5C PHE* 2.9 69.6 + - + +
7C LEU* 5.2 6.8 - - + +
98C SER* 4.3 13.1 + - - -
99C ALA 3.4 13.6 + - - +
100C SER* 3.8 14.0 - - - -
101C PHE* 4.6 0.4 - - - +
119C LEU* 1.3 74.6 - - - +
121C VAL* 1.3 83.2 + - - +
122C SER* 4.2 8.7 + - - -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LEU* 3.6 27.1 - - + -
3C ARG 3.4 3.6 - - - -
4C VAL* 3.9 20.2 - - + -
65C LEU* 4.0 15.5 - - + -
86C VAL* 4.6 4.0 - - + -
88C LEU* 4.1 6.5 - - + -
91C VAL* 3.8 23.5 - - + +
98C SER* 3.2 3.5 - - - -
99C ALA 2.8 32.1 + - - +
101C PHE* 4.3 11.9 - - + -
119C LEU* 4.1 11.2 - - + -
120C GLN* 1.3 84.4 + - - +
122C SER* 1.3 65.2 + - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.7 0.2 - - - +
2C LEU* 3.6 6.9 - - - +
3C ARG* 2.8 67.8 + - - +
91C VAL* 4.1 2.2 - - - -
96C SER 5.3 0.7 - - - -
97C LEU 3.2 13.2 - - - -
98C SER* 3.6 12.8 - - - +
120C GLN* 4.2 7.9 + - - -
121C VAL* 1.3 77.7 - - - +
123C TYR* 1.3 67.2 + - - +
124C THR* 3.9 3.6 - - - +
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.4 14.1 - - + -
0C PHE* 4.5 11.5 - - + -
1C MET 3.6 2.5 - - - -
2C LEU* 3.9 16.6 - - + +
28C PHE* 5.5 1.4 - + - -
54C LEU* 3.3 36.3 - - + -
59C LEU* 3.3 29.3 - - + +
88C LEU* 3.6 19.6 - - - +
91C VAL* 3.5 32.1 - - + -
92C LEU* 3.4 30.2 - - + +
96C SER 5.1 1.0 - - - +
97C LEU* 2.9 38.1 + - + +
122C SER* 1.3 75.0 - - - +
124C THR* 1.3 66.7 + - - +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C PHE* 3.3 10.3 - - - -
1C MET* 2.8 43.2 + - - +
3C ARG* 3.1 52.9 + - - +
51C GLU* 5.1 2.8 + - - -
122C SER* 3.9 4.9 - - - +
123C TYR* 1.3 81.6 - - - +
125C ALA* 1.3 67.9 + - - +
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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