Contacts of the strand formed by residues 125 - 130 (chain G) in PDB entry 2HAK
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 125 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82G LYS 3.6 1.2 - - - +
83G ILE* 3.6 2.1 - - - -
84G ILE* 2.7 46.7 + - + +
86G LYS* 3.7 17.0 - - + +
97G LEU* 3.5 38.8 - - + -
98G PHE* 4.8 9.0 - - + -
101G VAL* 4.2 8.3 - - + -
118G VAL* 3.9 27.8 - - + -
119G ILE 3.5 2.2 - - - +
120G GLU* 4.0 19.7 - - + +
124G THR* 1.3 73.2 + - - +
126G TYR* 1.3 61.3 + - - +
127G LEU* 3.9 27.4 - - + -
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Residues in contact with TYR 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 3.7 38.6 - - + +
55G LEU* 6.5 0.4 - - + -
81G VAL* 4.0 15.7 - - + -
82G LYS 3.4 3.1 - - - -
83G ILE* 3.7 36.0 - - + +
117G GLU 3.6 0.9 - - - +
118G VAL* 3.4 5.7 - - - -
119G ILE* 2.5 69.8 + - + +
121G THR* 4.6 6.1 - - + -
124G THR* 3.4 40.2 + - + +
125G LEU* 1.3 73.0 - - - +
127G LEU* 1.3 64.6 + - - +
128G VAL* 3.9 1.9 + - + +
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ALA 3.5 2.1 - - - +
81G VAL* 3.1 4.2 - - - -
82G LYS* 2.7 47.1 + - + +
84G ILE* 4.4 18.4 - - + -
97G LEU* 5.4 2.9 - - + -
100G GLU* 6.0 0.7 - - - +
101G VAL* 3.7 35.0 - - + -
104G MET* 4.1 24.9 - - + -
115G LEU* 4.1 7.2 - - + -
117G GLU 3.6 1.8 - - - -
118G VAL* 4.3 16.8 - - + -
125G LEU* 3.9 21.3 - - + -
126G TYR* 1.3 76.6 - - - +
128G VAL* 1.3 61.9 + - - +
129G MET* 3.6 18.0 + - + +
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G TYR* 3.4 52.9 - - + +
79G VAL* 3.6 19.3 - - + -
80G ALA 3.5 2.7 - - - +
81G VAL* 4.4 14.8 - - + +
115G LEU* 3.7 2.3 - - - +
116G PHE* 2.6 38.8 + - + +
117G GLU* 2.8 29.3 + - + +
119G ILE* 4.7 8.1 - - + -
126G TYR 4.7 4.0 - - - +
127G LEU* 1.3 75.1 - - - +
129G MET* 1.3 56.1 + - - +
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Residues in contact with MET 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G VAL* 6.2 1.3 - - - -
79G VAL* 3.4 7.1 - - - +
80G ALA* 2.8 47.8 + - + +
82G LYS* 5.1 15.5 - - + -
104G MET* 3.7 31.0 - - + +
113G VAL* 4.7 15.7 - - + +
114G LYS 3.3 16.4 - - - +
115G LEU* 3.9 9.0 - - + -
116G PHE* 3.5 9.2 - - - -
127G LEU* 3.6 33.7 - - + +
128G VAL* 1.3 73.1 - - - +
130G GLU* 1.3 69.7 + - + +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ALA* 4.0 3.3 - - - +
112G ILE 3.2 6.1 - - - +
113G VAL* 3.2 25.3 - - + +
114G LYS* 2.9 32.3 + - - +
116G PHE* 3.3 21.0 - - + -
129G MET* 1.3 86.0 - - - +
131G TYR* 1.3 68.0 + - - +
132G ALA 4.0 1.2 + - - -
184G ASP* 4.9 1.5 - - + +
190G LYS* 2.9 39.1 + - + -
363G ARG* 3.0 24.2 + - - +
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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