Contacts of the strand formed by residues 113 - 119 (chain A) in PDB entry 4HH3
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 ILE 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU 3.7 1.2 - - - +
28A LEU* 3.7 3.4 - - - -
29A VAL* 2.7 49.2 + - + +
30A SER 5.6 3.8 - - - +
31A GLN* 6.2 0.4 - - - -
70A PHE* 3.9 16.4 - - + -
74A SER* 3.5 31.6 - - - +
77A LEU* 4.9 3.1 - - + -
104A LEU* 4.0 16.6 - - + -
105A HIS 3.3 10.5 - - - +
106A ARG* 3.8 32.5 - - - +
112A SER* 1.3 77.6 - - - +
114A LEU* 1.3 64.6 + - - +
115A MET* 3.9 19.9 + - + +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.0 15.5 - - + -
26A SER* 4.5 2.9 - - - -
27A LEU 3.5 19.5 - - - +
28A LEU* 4.3 9.9 - - + -
39A MET* 4.3 20.6 - - - -
103A ILE 3.6 2.3 - - - +
104A LEU* 3.6 2.1 - - - -
105A HIS* 2.9 35.7 + - + +
107A LEU* 4.1 21.9 - - + +
112A SER 4.2 0.8 - - - -
113A ILE* 1.3 72.9 - - - +
115A MET* 1.3 61.0 + - - +
116A LEU* 3.7 26.8 + - + -
7B LEU* 4.4 9.6 - - + -
18B LEU* 3.8 31.4 - - + -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 3.1 10.0 - - - -
27A LEU* 2.8 45.8 + - + +
29A VAL* 3.7 25.1 - - - -
58A LEU* 3.9 12.1 - - + -
70A PHE* 3.9 20.0 - - + -
88A LEU* 3.6 31.0 - - + -
90A HIS* 5.4 0.7 - - + +
102A TYR* 3.5 30.3 - - + -
103A ILE 3.6 4.7 - - - -
104A LEU* 3.8 15.5 - - + -
113A ILE* 4.0 11.7 - - + +
114A LEU* 1.3 76.3 - - - +
116A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.7 29.6 - - + -
23A ALA* 4.3 6.3 - - + -
25A ILE 4.2 1.3 - - - -
26A SER* 4.1 6.1 - - - -
101A ARG 3.8 1.2 - - - +
102A TYR* 3.3 3.9 - - - -
103A ILE* 3.0 40.3 + - + +
105A HIS* 3.7 19.5 - - + +
114A LEU* 3.7 18.8 - - + +
115A MET* 1.3 72.5 - - - +
117A GLY* 1.3 60.3 + - - +
118A ARG* 5.2 3.3 + - - -
18B LEU* 3.4 34.3 - - + +
21B THR* 3.6 14.1 - - - +
22B ALA* 3.9 19.3 - - + -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.8 3.6 - - - +
24A ASP* 2.9 32.9 + - - +
25A ILE* 2.8 21.9 + - - -
100A ILE* 3.6 17.0 - - - -
101A ARG 3.5 5.6 - - - -
102A TYR* 3.6 4.6 - - - -
116A LEU* 1.3 74.7 - - - +
118A ARG* 1.3 63.9 + - - +
119A ASP 4.2 0.2 - - - -
22B ALA 5.4 0.2 - - - +
118B ARG* 4.2 0.2 + - - -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 3.5 4.5 - - - +
100A ILE* 3.4 5.0 - - - +
101A ARG* 2.9 77.8 + - + +
103A ILE* 4.4 14.8 - - - +
116A LEU 5.2 4.2 + - - -
117A GLY* 1.3 76.7 - - - +
119A ASP* 1.3 65.1 + - - +
120A LEU* 3.4 4.3 + - + +
21B THR 2.9 21.8 + - - -
22B ALA* 3.2 21.9 + - - +
23B ALA 3.2 14.8 + - - -
24B ASP* 2.7 30.7 + - - +
118B ARG* 3.7 20.0 - - - +
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Residues in contact with ASP 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 2.9 14.2 + - + +
44A HIS* 2.8 35.0 + - + +
45A PRO* 5.0 1.4 - - - +
47A PHE* 3.6 14.2 - - + -
100A ILE* 3.8 8.6 - - - +
118A ARG* 1.3 70.5 - - - +
120A LEU* 1.3 63.0 + - - +
121A ARG* 2.9 55.4 + - - +
122A PRO* 3.9 8.0 - - + +
123B ILE* 3.8 23.2 - - + +
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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