Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 3S4S
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 ASN 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.6 7.0 - - - -
94A ASN* 2.8 20.2 + - - +
95A SER* 3.2 37.3 + - - -
96A PRO 3.3 12.7 + - - -
97A VAL* 3.5 17.9 - - - +
98A GLU 4.8 0.6 - - - +
101A GLU* 3.4 3.6 + - - +
102A PRO* 1.3 74.5 + - - +
104A VAL* 1.3 83.3 + - - +
152A PRO* 3.5 1.6 - - - +
153A PHE* 2.9 44.2 + - + -
155A PRO* 4.0 9.6 - - + -
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Residues in contact with VAL 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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93A THR* 3.3 2.3 - - - -
94A ASN* 2.9 47.2 + - + +
103A ASN* 1.3 92.2 + - - +
105A LEU* 1.3 71.9 + - - +
106A ILE* 3.5 3.7 + - + +
150A TYR* 4.1 27.4 - - + -
151A LEU 3.6 10.8 - - - +
152A PRO* 4.2 14.4 - - + -
153A PHE* 3.5 3.8 - - - -
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Residues in contact with LEU 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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91A VAL* 3.5 28.3 - - + -
92A LEU 3.6 7.6 - - - +
93A THR* 4.6 2.5 - - + +
104A VAL* 1.3 71.8 - - - +
106A ILE* 1.3 58.9 + - - +
121A TRP* 3.5 21.1 - - + -
150A TYR* 3.5 5.9 - - - -
151A LEU* 2.9 42.9 + - + +
153A PHE* 3.4 19.3 - - + -
161A TYR* 3.4 49.8 - - + -
178A TRP* 3.7 26.0 - - + -
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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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91A VAL* 3.2 6.6 - - - +
92A LEU* 2.6 55.9 + - + +
93A THR 4.4 2.2 - - - +
94A ASN* 3.5 25.8 - - + +
104A VAL* 3.7 10.1 - - + +
105A LEU* 1.3 77.0 - - - +
107A CYS* 1.3 64.4 + - - +
108A PHE 4.5 0.4 - - - +
121A TRP* 3.9 2.2 - - - -
148A PHE* 4.1 26.7 - - + -
149A HIS 3.8 3.6 - - - +
150A TYR* 4.2 20.9 - - + -
150B ASN* 3.4 36.6 - - + +
152B ASP* 5.9 0.7 - - - +
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Residues in contact with CYS 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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89A VAL* 3.9 18.2 - - - -
90A THR 3.7 2.7 - - - -
91A VAL* 4.5 2.0 - - - +
106A ILE* 1.3 74.8 - - - +
108A PHE* 1.3 58.0 + - - +
109A ILE* 3.2 23.8 - - + +
121A TRP* 3.5 19.4 - - + -
148A PHE* 3.6 4.0 - - - -
149A HIS* 3.1 31.5 + - + +
163A CYS* 2.0 50.0 - - + -
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Residues in contact with PHE 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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88A GLU 3.4 2.1 - - - +
89A VAL* 3.4 4.7 - - - -
90A THR* 2.8 56.6 + - + +
92A LEU* 4.8 10.8 - - + -
106A ILE* 3.9 0.8 - - + -
107A CYS* 1.3 73.1 - - - +
109A ILE* 1.3 63.2 + - - +
110A ASP* 3.5 36.1 + - + -
146A ARG* 3.8 33.7 - - + -
147A LYS 3.7 5.2 - - - -
148A PHE* 3.6 39.7 - + + -
149B GLN 5.7 2.5 - - - -
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Residues in contact with ILE 109 (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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87A PRO* 3.4 33.2 - - + -
88A GLU 3.5 3.4 - - - -
89A VAL* 4.3 5.2 - - + -
107A CYS* 3.2 33.0 - - - +
108A PHE* 1.3 73.5 - - - +
110A ASP* 1.3 58.5 + - - +
112A PHE* 3.5 19.3 - - + -
117A VAL* 4.6 10.1 - - + -
119A VAL* 4.3 8.5 - - + -
146A ARG* 3.3 3.8 - - - +
147A LYS* 2.9 40.2 + - + +
149A HIS* 4.0 20.0 - - - +
165A VAL* 4.1 20.6 - - + -
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Residues in contact with ASP 110 (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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87A PRO* 3.3 3.8 - - - +
88A GLU* 2.7 43.7 + - + +
90A THR* 6.1 0.9 - - + -
108A PHE* 3.5 33.1 - - + -
109A ILE* 1.3 75.2 - - - +
111A LYS* 1.3 105.9 + - + +
112A PHE* 3.6 1.3 - - - -
140A ARG* 3.1 26.5 + - - -
145A PHE 3.5 2.9 - - - -
146A ARG* 3.1 15.6 - - - +
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Residues in contact with LYS 111 (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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85A VAL* 3.7 5.1 - - + +
86A PRO 3.3 13.4 - - - +
88A GLU* 3.6 40.3 + - + +
110A ASP* 1.3 104.1 + - + +
112A PHE* 1.3 55.3 + - - +
140A ARG* 3.8 26.0 - - - +
142A ASP* 5.0 0.7 - - - -
144A LEU* 3.4 34.0 - - + +
145A PHE 2.9 9.2 + - - -
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Residues in contact with PHE 112 (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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85A VAL* 3.0 19.1 - - - +
87A PRO* 3.5 34.5 - - + -
109A ILE* 3.5 29.6 - - + -
110A ASP 3.7 4.0 - - - -
111A LYS* 1.3 73.8 - - - +
113A THR* 1.3 66.5 + - - +
114A PRO 3.7 11.0 - - - -
115A PRO* 4.3 0.9 - - + -
116A VAL 4.6 1.1 - - - -
117A VAL* 4.6 7.0 - - + -
137A PHE* 3.9 36.1 - + - -
144A LEU* 3.6 3.8 - - - +
145A PHE* 2.9 51.1 + - + -
146A ARG* 4.3 1.6 - - - -
147A LYS* 4.4 6.1 - - + -
167A HIS* 3.6 20.0 - + - +
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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