Contacts of the strand formed by residues 112 - 124 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0D PHE* 3.5 28.1 - - + -
97D LEU* 3.5 31.9 - - + -
123D TYR* 3.4 47.1 - - + -
104F PRO* 5.7 1.1 - - + -
105F LEU 3.7 1.1 - - - +
106F LEU* 3.6 23.6 - - + -
107F ASP* 4.8 1.2 - - - +
110F LYS 4.2 0.2 - - - +
111F GLN* 1.3 88.9 - - + +
113F THR* 1.3 60.8 + - - +
114F GLY 3.4 2.9 - - - +
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Residues in contact with THR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASN 5.2 1.7 - - - +
81F LEU 3.3 26.8 + - - +
82F GLY* 4.8 0.2 - - - -
105F LEU* 2.9 19.2 + - - +
106F LEU 3.9 0.9 - - - -
107F ASP* 3.5 35.2 - - + +
112F PRO* 1.3 73.6 - - - +
114F GLY* 1.3 57.1 + - - +
115F ALA* 3.2 24.8 + - - +
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Residues in contact with GLY 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 5.8 4.7 - - - -
11F ASN* 3.6 24.6 - - - +
105F LEU 4.5 0.2 + - - -
112F PRO* 3.4 7.0 - - - +
113F THR* 1.3 78.3 - - - +
115F ALA* 1.3 62.8 + - - +
116F SER* 4.1 0.9 + - - -
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F GLU 3.3 10.8 - - - +
11F ASN 3.6 17.4 + - - +
12F VAL* 4.1 11.2 - - + -
81F LEU 6.5 0.4 - - - -
82F GLY* 6.2 0.2 - - - -
104F PRO* 3.5 5.7 - - - +
105F LEU* 2.8 40.0 + - + +
113F THR* 3.2 17.0 + - - +
114F GLY* 1.3 82.2 + - - +
116F SER* 1.3 61.6 + - - +
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Residues in contact with SER 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PRO* 4.0 21.7 - - - +
9F ALA* 3.2 7.1 - - - +
10F GLU* 2.9 48.6 + - - +
11F ASN* 5.1 2.1 + - - -
102F ASN* 3.5 19.6 + - - -
103F ALA 3.2 14.1 - - - -
104F PRO* 4.2 1.1 - - - -
105F LEU* 4.2 5.1 - - - +
114F GLY 4.1 0.8 + - - -
115F ALA* 1.3 75.7 - - - +
117F LEU* 1.3 60.5 + - - +
118F VAL* 5.4 0.8 - - - +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 4.0 13.2 - - + -
8F TYR 3.6 14.8 - - - +
9F ALA* 4.1 4.9 - - + -
24F CYS* 4.2 8.1 - - - -
46F TRP* 3.7 24.2 - - + -
67F VAL* 3.6 39.0 - - + -
69F VAL* 4.2 9.2 - - + -
84F ALA* 5.9 0.2 - - + -
101F PHE 3.4 3.1 - - - +
102F ASN* 3.5 0.6 - - - -
103F ALA* 2.7 35.5 + - + +
105F LEU* 4.0 18.2 - - + -
116F SER* 1.3 75.1 - - - +
118F VAL* 1.3 65.3 + - - +
119F LEU* 3.8 21.2 - - + +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 4.0 0.9 - - - -
7F LEU* 3.0 37.3 + - + -
8F TYR* 2.8 64.9 + - + +
10F GLU* 5.5 0.7 - - + -
101F PHE 3.3 2.7 - - - +
102F ASN* 3.5 32.3 - - + +
116F SER* 5.4 2.0 - - - +
117F LEU* 1.3 75.1 - - - +
119F LEU* 1.3 67.7 + - - +
201F FMT 3.8 24.5 - - - -
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Residues in contact with LEU 119 (chain F).
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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4F VAL* 4.2 9.4 - - + -
5F PHE 3.2 15.5 - - - +
6F ILE* 4.3 7.6 - - + -
7F LEU* 4.4 2.9 - - - +
65F LEU* 3.6 30.7 - - + -
67F VAL* 4.1 14.6 - - + -
86F VAL* 4.3 13.0 - - + -
100F SER* 3.4 3.8 - - - -
101F PHE* 2.8 64.4 + - + +
103F ALA* 5.1 3.4 - - + -
117F LEU* 3.8 27.6 - - + +
118F VAL* 1.3 80.1 - - - +
120F GLN* 1.3 59.5 + - - +
121F VAL* 4.3 5.2 - - + -
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Residues in contact with GLN 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ARG* 4.7 0.5 - - - +
4F VAL* 3.4 3.1 - - - -
5F PHE* 2.9 62.3 + - + +
7F LEU* 4.9 9.8 - - + +
98F SER* 3.7 28.9 + - - -
99F ALA 3.6 12.9 + - - +
100F SER* 4.3 9.6 - - - -
119F LEU* 1.3 74.3 - - - +
121F VAL* 1.3 69.4 + - - +
122F SER* 4.1 7.9 + - - -
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F LEU* 3.6 27.4 - - + -
3F ARG 3.4 7.2 - - - +
4F VAL* 3.9 20.9 - - + -
65F LEU* 4.1 15.5 - - + -
86F VAL* 5.1 0.2 - - + -
88F LEU* 3.8 16.4 - - + -
91F VAL* 3.9 12.0 - - + +
98F SER* 3.2 2.9 - - - -
99F ALA 2.7 42.3 + - - +
101F PHE* 4.2 16.4 - - + -
119F LEU* 4.3 7.6 - - + -
120F GLN* 1.3 81.6 + - - +
122F SER* 1.3 65.1 + - - +
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Residues in contact with SER 122 (chain F).
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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1F MET 3.6 0.3 - - - +
2F LEU* 3.6 7.2 - - - +
3F ARG* 2.8 74.7 + - - +
91F VAL* 4.4 4.0 - - - -
96F SER 5.4 0.7 - - - -
97F LEU 3.3 5.6 - - - -
98F SER* 3.5 20.2 - - - +
120F GLN* 4.1 8.4 + - - -
121F VAL* 1.3 76.8 - - - +
123F TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E GLN* 4.1 12.5 + - + +
112E PRO* 3.6 44.2 + - + +
0F PHE* 3.2 47.7 - + + +
1F MET 3.5 3.6 - - - -
2F LEU* 4.9 3.6 - - + +
3F ARG* 5.3 0.3 + - - -
54F LEU* 3.4 35.2 - - + -
59F LEU* 3.7 18.2 - - + -
91F VAL* 4.1 8.6 - - + +
92F LEU* 5.4 0.4 - - + -
96F SER 5.3 1.0 - - - +
97F LEU* 2.9 39.9 + - + +
122F SER* 1.3 75.7 + - - +
124F THR* 1.3 65.5 + - - +
125F ALA 5.2 0.4 - - - -
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Residues in contact with THR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F PHE* 3.2 2.6 - - - -
1F MET* 2.4 60.3 + - + +
3F ARG* 3.5 47.9 + - + +
51F GLU* 4.1 10.5 - - - +
123F TYR* 1.3 83.0 - - - +
125F ALA* 1.3 62.5 + - - +
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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