Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 2DYY
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 ALA 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE 2.8 17.0 + - - +
74A LYS* 3.3 12.6 - - + -
75A VAL* 2.9 26.7 + - - +
101A PRO* 1.3 72.3 - - - +
103A ARG* 1.3 59.2 + - - +
18B SER 3.7 13.7 - - - +
20B ALA* 4.7 0.2 - - - -
21B ILE* 3.4 11.1 - - + +
28B PHE* 3.7 23.6 - - + +
29B ILE 4.4 0.4 - - - -
30B ALA* 4.0 16.4 - - + +
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Residues in contact with ARG 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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74A LYS* 5.8 0.2 - - - -
75A VAL* 3.3 7.0 - - + +
77A VAL* 3.9 22.4 - - - -
88A MET* 4.3 11.3 - - - +
89A ASN* 3.0 33.3 + - - +
92A TYR* 3.3 42.6 - - + +
101A PRO 3.3 0.6 + - - -
102A ALA* 1.3 73.2 - - - +
104A VAL* 1.3 67.9 + - - +
105A ALA* 4.1 15.4 - - - +
15B GLY* 5.2 0.8 - - - -
16B PRO* 4.2 6.1 - - - +
17B TYR* 3.4 55.8 - - + +
30B ALA* 3.3 9.2 - - - +
31B GLY* 2.7 31.5 + - - +
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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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74A LYS* 5.5 4.0 - - + -
75A VAL 3.0 6.0 + - - +
76A THR* 3.9 27.1 - - + +
77A VAL* 2.8 28.6 + - - +
103A ARG* 1.3 82.6 - - - +
105A ALA* 1.3 66.0 + - - +
106A VAL* 5.1 2.0 - - + +
29B ILE 4.9 0.9 - - - +
30B ALA* 4.3 1.3 - - - -
31B GLY* 3.3 17.3 - - - +
78B TYR* 4.1 26.5 - - + +
118B GLU* 4.2 10.3 - - - +
120B GLU* 3.5 30.7 - - + +
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Residues in contact with ALA 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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77A VAL* 3.6 12.1 - - + +
79A LEU* 5.1 4.5 - - + -
85A PHE* 6.5 1.8 - - + -
88A MET* 5.0 6.3 - - + -
103A ARG* 4.1 22.4 - - - +
104A VAL* 1.3 76.2 - - - +
106A VAL* 1.3 60.8 + - - +
107A GLU* 6.0 0.2 - - - -
112B PRO* 3.1 25.9 - - + +
118B GLU* 2.9 24.6 + - - +
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Residues in contact with VAL 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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76A THR* 5.6 0.2 - - + -
77A VAL 3.1 8.0 + - - +
78A TYR* 3.5 29.6 - - + -
79A LEU* 3.1 22.2 + - - +
104A VAL* 5.4 4.0 - - + -
105A ALA* 1.3 76.2 - - - +
107A GLU* 1.3 66.0 + - - +
108A VAL* 4.3 7.9 - - + -
78B TYR* 4.2 23.3 - - + -
108B VAL* 3.4 23.1 - - + -
110B ARG 4.2 2.5 - - - -
111B LEU* 3.3 31.2 - - + -
112B PRO* 4.7 1.8 - - - -
118B GLU* 4.3 3.1 - - - +
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Residues in contact with GLU 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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79A LEU* 3.3 25.1 - - + -
81A ASP* 3.9 30.9 - - - +
83A ASN* 4.9 0.8 - - - +
85A PHE* 4.6 13.7 - - - +
106A VAL* 1.3 75.9 - - - +
108A VAL* 1.3 61.2 + - - +
108B VAL* 3.4 9.2 - - - +
109B SER* 3.2 22.2 + - - -
110B ARG* 3.1 65.4 + - + +
111B LEU 4.0 14.9 - - - +
112B PRO* 4.3 6.8 - - - +
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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