Contacts of the strand formed by residues 114 - 125 (chain G) in PDB entry 5M64
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 GLY 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G SER* 3.1 5.4 - - - -
49G LEU* 2.9 40.7 + - - +
105G ILE* 4.1 8.5 - - - -
106G LYS 3.6 10.1 - - - -
107G ILE* 3.6 12.3 - - - +
112G PRO 3.9 1.6 + - - -
113G PHE* 1.3 75.0 - - - +
115G PHE* 1.3 63.2 + - - -
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Residues in contact with PHE 115 (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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6A PRO* 5.6 2.5 - - + -
7A VAL* 3.2 27.8 - - + -
8A GLY* 4.6 12.3 - - - -
9A SER* 5.5 0.9 - - - -
10A GLU* 4.4 18.4 - - + -
47G VAL 3.8 5.2 - - - +
48G SER* 3.2 28.7 - - - -
105G ILE* 3.6 7.5 - - - +
106G LYS* 2.9 47.9 + - - +
108G THR* 3.2 30.7 - - + -
111G THR* 5.0 6.5 - - + -
113G PHE* 4.8 3.8 - - + -
114G GLY* 1.3 74.8 - - - -
116G THR* 1.3 59.8 + - - +
117G TRP* 4.6 16.2 + + + +
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Residues in contact with THR 116 (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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45G LEU 4.3 0.2 - - - +
47G VAL* 2.8 48.1 + - + +
49G LEU* 3.6 28.3 - - + -
61G VAL* 6.2 1.1 - - + -
89G ILE* 3.3 33.2 - - + +
90G LEU 4.1 4.2 + - - -
105G ILE* 3.4 14.5 - - - +
114G GLY 3.9 1.0 + - - -
115G PHE* 1.3 72.8 - - - +
117G TRP* 1.3 71.8 + - - +
118G CYS* 4.1 10.0 + - - -
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Residues in contact with TRP 117 (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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1201B GLU* 5.6 4.9 - - + -
1202B PRO* 3.9 28.6 - - + +
65F ARG* 3.2 46.9 - - - +
45G LEU 3.9 4.7 - - - -
46G TYR* 3.3 42.7 - + + +
47G VAL 4.7 1.1 + - - -
90G LEU* 3.4 27.7 + - - +
106G LYS* 5.7 11.4 - - - -
115G PHE* 4.6 16.1 - + + +
116G THR* 1.3 92.3 + - - +
118G CYS* 1.3 60.2 + - - +
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Residues in contact with CYS 118 (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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44G ALA* 4.8 1.3 - - - -
45G LEU* 2.8 58.3 + - - +
47G VAL* 4.8 2.7 - - - -
61G VAL* 5.7 8.1 - - - -
88G LYS 3.3 18.2 - - - +
89G ILE* 3.8 20.0 - - + -
90G LEU* 3.7 4.5 - - - -
116G THR* 4.5 14.6 - - - -
117G TRP* 1.3 73.5 - - - +
119G HIS* 1.3 61.0 + - - +
120G VAL* 4.7 10.2 - - + +
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Residues in contact with HIS 119 (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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25D THR* 4.3 15.9 - - + +
62F GLU* 6.0 0.4 + - - -
42G PRO* 6.3 2.7 - - + -
43G ILE 3.4 11.0 - - - +
44G ALA* 4.0 13.0 - - + +
86G GLY 3.7 5.9 - - - +
88G LYS* 3.4 33.9 + - + +
90G LEU* 3.3 40.4 - - + +
118G CYS* 1.3 73.1 - - - +
120G VAL* 1.3 69.5 + - - +
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Residues in contact with VAL 120 (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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42G PRO* 4.5 1.8 - - - -
43G ILE* 2.8 47.3 + - + +
45G LEU* 4.5 16.6 - - + -
66G LEU* 6.0 3.1 - - + -
85G GLU 4.1 4.5 - - - +
86G GLY 3.5 18.2 - - - +
87G LEU* 3.7 29.6 - - + -
88G LYS 4.0 4.9 - - - +
118G CYS* 4.7 9.6 - - - +
119G HIS* 1.3 83.5 - - - +
121G ASN* 1.3 59.6 + - - +
122G LEU* 3.6 20.4 - - + -
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Residues in contact with ASN 121 (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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40G ARG* 3.5 22.1 + - - +
41G VAL 3.2 14.4 - - - +
42G PRO* 3.7 27.4 - - + +
84G TYR* 3.9 0.2 - - - -
85G GLU* 2.8 69.5 + - - +
86G GLY* 4.5 2.5 + - - -
120G VAL* 1.3 69.4 - - - +
122G LEU* 1.3 63.7 + - - +
123G TYR* 4.9 0.4 - - - -
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Residues in contact with LEU 122 (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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41G VAL* 2.9 35.8 + - - +
43G ILE* 3.8 23.8 - - + -
45G LEU* 6.0 1.6 - - + -
66G LEU* 4.7 8.3 - - + -
69G LEU* 4.2 25.4 - - + -
70G VAL* 5.9 1.8 - - + -
81G VAL* 4.4 15.3 - - + -
83G GLY 3.3 20.2 - - - +
84G TYR* 3.7 20.2 - - + -
120G VAL* 3.5 31.5 + - + -
121G ASN* 1.3 78.2 - - - +
123G TYR* 1.3 67.3 + - - +
124G VAL* 4.4 2.1 - - + +
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Residues in contact with TYR 123 (chain G).
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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36D VAL* 6.3 0.7 - - + -
39D PHE* 3.3 36.6 - + + +
40D LEU* 5.4 7.0 - - + -
43D PHE* 6.4 0.7 - + - -
38G ILE* 5.5 2.2 - - + -
39G VAL 3.8 5.6 - - - +
40G ARG* 3.2 54.3 - - + +
81G VAL* 3.1 13.5 - - - +
82G LEU* 3.0 45.0 + - + +
83G GLY* 2.7 26.6 + - - +
84G TYR 4.3 5.8 + - - -
85G GLU* 3.3 40.0 - - + +
121G ASN* 4.7 1.1 - - - -
122G LEU* 1.3 75.6 - - - +
124G VAL* 1.3 62.1 + - - +
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Residues in contact with VAL 124 (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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38G ILE* 3.9 2.2 - - - +
39G VAL* 2.7 59.0 + - + +
41G VAL* 3.7 20.2 - - + -
77G VAL* 3.6 25.1 - - + +
79G GLY* 3.5 34.8 - - - +
80G VAL 3.2 10.3 - - - +
81G VAL* 4.1 4.7 - - + +
82G LEU* 4.1 4.2 - - - +
122G LEU* 4.4 2.0 - - + +
123G TYR* 1.3 78.2 - - - +
125G TRP* 1.3 62.5 + - - +
126G GLN* 3.5 7.9 - - - +
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Residues in contact with TRP 125 (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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37G CYS* 2.7 57.5 - - + +
38G ILE* 3.6 14.5 - - + +
79G GLY* 3.5 0.3 - - - -
80G VAL* 2.7 44.7 + - + +
82G LEU* 3.7 22.0 - - + -
124G VAL* 1.3 73.8 - - - +
126G GLN* 1.3 60.5 + - - +
127G PRO* 3.6 40.4 - - + +
133G LEU* 4.5 13.5 - - + -
149G ILE* 3.9 22.3 - - + +
153G PHE* 3.4 39.9 - + + -
243G VAL* 5.8 0.9 - - + -
245G VAL* 4.2 17.9 - - + -
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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