Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 4S0H
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 LYS 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LYS 4.6 4.3 - - - +
98A THR* 1.3 86.7 - - - +
100A TYR* 1.3 60.7 - - - +
142A PRO* 4.1 34.7 + - + +
143A ALA* 3.5 11.7 - - - +
144A THR* 4.5 15.3 - - + +
187A LYS* 3.7 1.2 - - - +
188A ALA* 3.0 37.0 + - + -
158B LYS* 5.5 3.2 - - - +
129E PRO* 6.0 1.2 - - - +
130E ALA* 4.9 12.5 - - - +
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Residues in contact with TYR 100 (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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54A ILE* 4.9 8.2 - - + +
94A LEU* 3.6 22.3 - - + +
95A ASN* 3.3 29.6 + - - +
98A THR* 3.4 44.6 + - + +
99A LYS* 1.3 78.0 - - - +
101A ILE* 1.3 67.6 + - - +
102A LEU* 4.3 4.7 - - + -
142A PRO* 3.2 5.6 - - - +
143A ALA 2.9 29.3 + - - -
145A GLY* 3.8 12.8 - - - -
148A TRP* 3.3 20.4 + + + +
185A ILE* 3.6 25.6 - - + -
186A VAL 3.3 11.0 - - - +
187A LYS* 4.0 20.8 - - + -
188A ALA 4.3 0.4 - - - +
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Residues in contact with ILE 101 (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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100A TYR* 1.3 76.5 - - - +
102A LEU* 1.3 65.6 + - - +
103A LEU* 3.6 24.9 - - + -
137A VAL* 3.9 7.2 - - + -
141A SER* 3.5 21.8 - - - +
142A PRO* 4.3 9.0 - - + -
184A HIS 3.6 1.0 - - - +
185A ILE* 3.6 2.8 - - - -
186A VAL* 2.6 47.5 + - + +
187A LYS 4.6 0.2 - - - +
188A ALA* 4.0 19.7 - - + +
105E ASP* 4.2 7.9 - - - +
107E VAL* 4.9 3.8 - - + -
133E GLY* 5.7 5.2 - - - +
135E LEU* 6.3 1.3 - - + -
182E ARG* 3.8 25.8 - - - +
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Residues in contact with LEU 102 (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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89A VAL* 5.6 0.2 - - + -
91A VAL* 4.5 9.4 - - + -
94A LEU* 5.3 1.6 - - + -
100A TYR* 4.3 5.4 - - + -
101A ILE* 1.3 79.5 - - - +
103A LEU* 1.3 62.2 + - - +
137A VAL 3.9 0.2 - - - -
138A HIS* 2.8 30.5 + - + +
141A SER* 3.2 8.3 + - - -
148A TRP* 3.5 46.8 - - + +
153A VAL* 3.8 34.5 - - + -
155A PHE* 4.2 4.5 - - + -
183A LEU* 3.9 19.7 - - + -
184A HIS 3.3 1.8 - - - -
185A ILE* 3.6 28.3 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.6 23.3 - - + -
102A LEU* 1.3 75.5 - - - +
104A MET* 1.3 61.7 + - - +
135A LEU* 3.7 31.0 - - + -
136A TYR 3.2 6.5 - - - +
137A VAL* 3.6 31.0 - - + -
155A PHE* 4.3 2.5 - - - -
183A LEU* 3.5 7.6 - - - +
184A HIS* 2.8 40.6 + - + +
186A VAL* 3.7 27.8 - - + -
201A PHE* 5.7 2.5 - - + -
103E LEU* 6.3 1.1 - - + -
135E LEU* 4.7 10.5 - - + -
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Residues in contact with MET 104 (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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83A MET* 4.4 7.2 - - - -
87A TYR* 3.4 56.1 - - + -
103A LEU* 1.3 75.2 - - - +
105A ASP* 1.3 69.3 + - - +
106A ILE* 4.8 5.6 - - + -
135A LEU* 3.7 6.2 - - - +
136A TYR* 2.8 39.2 + - + +
155A PHE* 3.7 24.4 - - + -
158A LEU* 3.5 29.2 - - + -
171A ILE* 4.7 1.6 - - + +
181A PRO* 3.8 14.6 - - + -
182A ARG 3.4 19.5 - - - +
183A LEU* 4.3 2.0 - - + +
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Residues in contact with ASP 105 (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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104A MET* 1.3 78.0 - - - +
106A ILE* 1.3 77.2 + - - +
107A VAL* 3.2 8.8 - - - +
134A ARG 3.9 14.3 - - - +
135A LEU* 4.0 14.6 - - + +
171A ILE* 4.9 1.3 - - - -
180A GLN 3.9 0.2 - - - +
181A PRO* 3.4 2.6 - - - +
182A ARG* 2.6 70.9 + - + +
184A HIS* 3.2 25.2 + - + +
101E ILE* 4.9 8.1 - - - +
186E VAL* 4.2 4.9 - - - +
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Residues in contact with ILE 106 (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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83A MET* 5.2 5.4 - - + -
104A MET* 4.8 4.9 - - + -
105A ASP* 1.3 85.5 + - - +
107A VAL* 1.3 68.4 + - - +
108A PRO* 4.6 1.4 - - - +
134A ARG 5.0 1.5 + - - +
158A LEU* 4.8 5.6 - - + -
160A LEU* 3.7 29.8 - - + -
171A ILE* 3.7 35.1 - - + +
173A LEU* 4.0 6.4 - - + +
179A TYR* 3.5 38.2 - - + -
180A GLN 3.7 8.5 - - - +
181A PRO* 4.5 7.6 - - + -
211A PHE* 4.4 15.3 - - + -
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Residues in contact with VAL 107 (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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105A ASP* 3.2 28.5 - - - +
106A ILE* 1.3 77.8 - - - +
108A PRO* 1.3 72.3 - - + +
179A TYR* 4.1 4.5 - - - -
180A GLN* 2.7 50.8 + - + +
182A ARG* 3.5 34.3 - - + +
101E ILE* 6.1 3.4 - - + -
187E LYS 5.0 3.4 - - - +
188E ALA* 5.0 8.3 - - + -
189E ASP* 4.2 15.9 - - - +
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Residues in contact with PRO 108 (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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106A ILE 4.6 1.3 - - - +
107A VAL* 1.3 89.5 - - + +
109A ALA* 1.3 60.1 + - - +
110A ASP* 3.7 16.1 - - - +
130A ALA* 6.2 3.8 - - + -
178A LYS 3.8 7.6 - - - +
179A TYR* 4.1 13.6 - - + -
180A GLN* 4.9 0.2 - - - +
99E LYS* 6.1 4.7 - - + +
188E ALA* 5.6 5.4 - - + -
189E ASP* 2.5 45.4 - - - +
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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