Contacts of the strand formed by residues 95 - 107 (chain A) in PDB entry 1DMN
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 GLN 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 VAL* 3.7 2.2 - - - -
92A TRP* 2.5 43.8 + - - +
93A ASN 3.2 3.4 + - - +
94A GLY* 1.3 78.2 - - - +
96A PRO* 1.4 69.4 - - + +
97A CYS* 3.7 2.8 - - - -
127A VAL* 4.5 32.8 - - + +
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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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90A MET 3.3 11.7 - - - +
91A VAL* 3.7 14.1 - - + -
94A GLY 4.0 5.4 - - - +
95A GLN* 1.4 92.1 - - + +
97A CYS* 1.3 62.3 + - - +
126A SER 4.0 4.9 - - - +
127A VAL* 4.1 10.9 - - - +
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Residues in contact with CYS 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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89A GLU* 3.5 6.1 - - - +
90A MET* 2.8 44.6 + - - +
92A TRP* 3.8 24.7 - - - -
95A GLN 3.7 9.9 - - - -
96A PRO* 1.3 75.6 - - - +
98A ALA* 1.3 63.5 + - - +
125A LEU* 4.2 9.2 - - + -
126A SER 3.3 11.9 - - - +
127A VAL* 2.8 35.9 - - + -
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Residues in contact with ALA 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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87A ARG* 3.1 37.5 - - - +
88A VAL 3.2 9.6 - - - +
89A GLU* 4.6 5.8 - - + +
90A MET* 4.8 0.7 - - - -
97A CYS* 1.3 76.6 - - - +
99A LEU* 1.3 61.2 + - - +
124A ASN 3.8 0.4 - - - +
125A LEU* 3.4 6.4 - - - +
126A SER* 2.9 39.7 + - - +
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Residues in contact with LEU 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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87A ARG* 3.3 3.5 - - - +
88A VAL* 2.8 42.6 + - + +
90A MET* 4.8 18.8 - - + -
98A ALA* 1.3 75.9 - - - +
100A ASP* 1.3 64.0 + - - +
101A VAL* 3.8 21.8 + - + +
120A TRP* 3.7 43.5 - - + -
121A SER 4.2 1.3 - - - +
124A ASN* 3.4 25.6 - - + +
125A LEU* 4.0 16.8 - - + +
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Residues in contact with ASP 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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71A THR* 5.5 1.7 + - - +
86A PHE 3.6 4.9 - - - +
87A ARG* 2.6 51.0 + - - +
98A ALA 5.7 0.2 - - - -
99A LEU* 1.3 72.5 - - - +
101A VAL* 1.3 61.5 + - - +
119A TYR 4.3 0.3 - - - +
120A TRP* 3.5 6.4 - - - +
124A ASN* 3.0 45.6 + - + +
126A SER* 5.2 2.3 + - - -
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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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40A ASP* 5.7 0.4 - - - +
85A PRO* 4.7 0.2 - - - +
86A PHE* 2.9 68.2 + - + +
88A VAL* 4.9 3.4 - - + -
99A LEU* 3.8 29.6 - - + +
100A ASP* 1.3 81.9 - - - +
102A ILE* 1.3 70.8 + - - +
103A ASP* 3.8 11.2 - - - +
118A ALA* 4.0 3.1 - - + -
119A TYR 3.6 6.1 - - - +
120A TRP* 3.7 27.4 - - + -
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Residues in contact with ILE 102 (chain A).
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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83A ALA* 4.9 3.4 - - + -
84A MET 3.4 16.6 - - - +
85A PRO* 4.0 16.2 - - + -
101A VAL* 1.3 80.2 - - - +
103A ASP* 1.3 70.6 + - - +
104A VAL* 4.4 12.3 - - + -
118A ALA* 3.5 1.0 - - - -
119A TYR* 2.8 50.5 + - + +
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Residues in contact with ASP 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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13A MET* 4.0 2.0 - - - +
16A TYR* 3.8 16.5 + - - -
40A ASP* 4.6 1.0 - - - +
83A ALA* 3.2 4.5 - - - +
84A MET* 3.1 44.6 + - + +
86A PHE* 3.5 29.3 - - + -
101A VAL* 3.8 2.1 - - - +
102A ILE* 1.3 73.6 - - - +
104A VAL* 1.3 61.2 + - - +
105A MET* 3.9 7.4 - - + +
116A MET* 3.7 27.3 - - - +
117A GLN 3.4 1.6 - - - -
118A ALA* 3.2 27.2 - - - +
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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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81A CYS* 5.7 6.1 - - + -
82A GLY 3.4 10.5 - - - +
83A ALA* 3.9 16.4 - - + -
102A ILE* 4.4 6.1 - - + -
103A ASP* 1.3 78.2 - - - +
105A MET* 1.3 66.9 + - - +
115A THR 4.0 0.2 - - - +
116A MET* 3.5 2.6 - - - -
117A GLN* 2.9 48.2 + - - +
119A TYR* 3.9 26.7 - - + -
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Residues in contact with MET 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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13A MET* 3.9 30.1 - - + -
16A TYR* 3.8 42.4 - - + -
80A GLY 3.8 0.7 - - - +
81A CYS* 3.4 6.0 - - - +
82A GLY 2.9 31.7 + - - +
84A MET* 4.0 4.5 - - + -
103A ASP* 3.9 7.0 - - - +
104A VAL* 1.3 83.9 - - - +
106A ARG* 1.3 60.4 - - - +
107A PHE* 4.1 15.6 - - + -
113A ILE* 3.8 28.3 - - + -
115A THR* 3.4 6.7 - - - +
116A MET* 3.7 27.8 - - + -
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Residues in contact with ARG 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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79A ASN* 5.0 15.4 + - - +
80A GLY 3.5 5.4 - - - +
81A CYS* 3.8 23.9 - - - -
105A MET* 1.3 76.0 - - - +
107A PHE* 1.3 65.9 + - - +
113A ILE* 3.7 2.3 - - - -
114A GLN* 2.8 50.2 + - - +
115A THR* 3.1 34.1 + - + +
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Residues in contact with PHE 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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3A LEU* 3.6 13.3 - - - +
4A PRO* 3.6 22.7 - - + -
9A VAL* 3.8 29.6 - - + -
12A LEU* 3.5 39.5 - - + -
13A MET* 3.7 24.2 - - + -
31A MET* 5.4 2.5 - - + -
80A GLY* 2.9 21.1 + - - +
105A MET* 4.1 22.4 - - + -
106A ARG* 1.3 86.6 - - - +
108A ASP* 1.3 61.5 + - - +
111A GLY 3.8 9.0 - - - -
112A ARG 3.2 15.9 - - - +
113A ILE* 3.8 17.7 - - + -
114A GLN* 4.4 5.5 - - - +
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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