Contacts of the strand formed by residues 95 - 105 (chain A) in PDB entry 2F1W
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.3 6.1 - - - -
92A VAL 3.0 18.1 + - - +
93A ARG* 3.1 15.7 - - + +
94A ASN* 1.3 84.1 - - - +
96A PRO* 1.3 66.0 - - + +
97A TRP* 3.1 26.4 - - + +
121A CYS* 3.8 16.2 - - - -
122A ASN* 3.7 30.7 - - - +
130A TRP* 4.2 14.6 - - + -
131A SER 4.5 5.2 - - - +
132A CYS* 3.8 29.2 - - + -
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Residues in contact with PRO 96 (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 PRO* 3.7 22.9 - - + -
90A CYS 3.9 3.1 - - - +
91A PHE* 3.7 21.1 - - + -
94A ASN 4.4 1.3 - - - +
95A LEU* 1.3 83.0 - - + +
97A TRP* 1.3 63.1 + - - +
98A LYS* 4.1 9.1 + - - +
120A GLN* 3.8 1.2 + - - +
121A CYS* 3.6 1.6 - - - -
122A ASN* 2.9 59.8 + - - +
123A ALA 5.1 0.7 - - - +
124A GLU* 5.9 5.8 - - + +
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Residues in contact with TRP 97 (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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71A PHE* 3.8 22.5 - - + -
88A PRO 3.9 0.5 - - - +
89A PRO* 3.5 0.9 - - - +
90A CYS 2.8 40.7 + - - +
92A VAL* 3.1 37.2 + - + +
93A ARG* 5.7 0.2 - - + -
95A LEU* 3.1 27.7 + - + +
96A PRO* 1.3 74.7 - - - +
98A LYS* 1.3 64.8 + - - +
119A LEU* 3.9 25.1 - - + -
120A GLN 3.2 5.4 - - - +
121A CYS* 3.5 39.3 - - + -
132A CYS* 4.0 12.1 - - + -
134A ALA* 3.7 18.8 - - + -
158A PHE* 3.7 28.5 - + - -
195A VAL* 4.1 14.1 - - + -
197A ALA* 3.7 20.2 - - + -
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Residues in contact with LYS 98 (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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71A PHE* 4.1 4.0 - - - -
86A LEU* 4.0 23.2 - - + +
87A SER* 3.4 28.6 + - - +
89A PRO* 4.0 29.3 - - + +
96A PRO* 4.8 8.7 - - - +
97A TRP* 1.3 80.6 - - - +
99A ILE* 1.3 64.6 + - - +
119A LEU* 3.6 5.0 - - - +
120A GLN* 2.8 57.8 + - - +
124A GLU* 3.1 32.6 + - - +
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Residues in contact with ILE 99 (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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71A PHE* 3.6 28.5 - - + +
73A PHE* 3.8 17.2 - - + +
85A VAL 3.7 1.0 - - - +
86A LEU* 3.4 6.1 - - - +
87A SER* 2.9 38.1 + - - +
98A LYS* 1.3 72.7 - - - +
100A MET* 1.3 63.2 + - - +
101A VAL* 3.7 20.0 - - + -
117A PHE* 3.6 20.4 - - + -
118A PHE 3.5 3.1 - - - -
191A PHE* 3.8 29.6 - - + +
193A VAL* 3.6 33.0 - - + -
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Residues in contact with MET 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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84A SER* 4.5 10.3 - - - +
85A VAL 3.5 5.6 - - - +
86A LEU* 3.3 30.1 - - + -
99A ILE* 1.3 73.0 - - - +
101A VAL* 1.3 64.0 + - - +
102A MET* 4.7 11.9 - - + -
116A GLY 3.8 0.5 - - - +
117A PHE* 3.5 6.1 + - - -
118A PHE* 2.8 49.6 + - + +
120A GLN* 3.7 37.5 - - + +
164A ASP* 3.7 30.5 - - - +
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Residues in contact with VAL 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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73A PHE* 4.2 8.7 - - + -
75A VAL* 4.3 2.7 - - + -
78A PHE* 4.2 3.1 - - + -
81A LEU* 4.0 17.4 - - + +
83A GLU 3.8 0.5 - - - +
84A SER* 3.2 1.9 + - - -
85A VAL* 2.8 49.3 + - + +
99A ILE* 3.7 19.1 - - + -
100A MET* 1.3 79.9 - - - +
102A MET* 1.3 65.8 + - - +
115A VAL* 4.2 7.2 - - + -
116A GLY 3.4 8.5 - - - +
117A PHE* 4.7 0.2 - - + -
191A PHE* 3.6 48.0 - - + -
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Residues in contact with MET 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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81A LEU* 4.3 2.9 - - - -
83A GLU 3.8 0.9 - - - -
84A SER* 3.4 38.1 - - - +
100A MET* 4.7 14.8 - - + -
101A VAL* 1.3 81.0 - - - +
103A PRO* 1.3 81.6 - - + +
104A ARG* 3.6 31.4 - - - +
115A VAL* 4.1 1.3 - - - -
116A GLY* 2.7 38.9 + - - -
118A PHE* 3.7 31.0 - - + -
173A TRP* 5.1 0.9 - - - -
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Residues in contact with PRO 103 (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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81A LEU* 3.9 24.9 - - + +
82A SER* 4.4 4.3 - - - -
83A GLU* 3.4 25.1 - - - +
102A MET* 1.3 90.8 - - + +
104A ARG* 1.3 67.9 + - - +
113A LYS* 3.8 19.3 - - + +
114A SER 3.6 6.3 - - - +
173A TRP* 3.8 20.9 - - + -
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Residues in contact with ARG 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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102A MET* 3.6 29.1 - - - +
103A PRO* 1.3 83.2 - - - +
105A PHE* 1.3 61.1 + - - +
106A TYR* 4.0 9.4 + - + -
113A LYS* 3.5 7.6 - - - +
114A SER* 2.9 35.5 + - - +
116A GLY* 3.9 6.3 - - - -
118A PHE* 3.5 31.3 - - - -
168A SER* 3.3 46.0 - - - +
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Residues in contact with PHE 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 ARG* 1.3 72.9 - - - +
106A TYR* 1.3 72.3 + - - +
107A PRO* 4.0 23.6 - - + +
112A GLN* 3.5 49.8 - - + -
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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