Contacts of the helix formed by residues 93 - 107 (chain A) in PDB entry 4KBQ
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 SER 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA* 5.9 1.7 - - - +
64A THR* 4.4 4.9 - - - +
86A ALA* 5.4 0.6 - - - +
87A LEU* 4.7 0.2 - - - -
90A ASP* 3.4 34.6 + - - -
91A GLY 3.4 2.0 - - - -
92A GLN* 1.3 76.9 - - - +
94A VAL* 1.3 62.5 + - - +
95A LYS* 3.6 3.8 + - - +
96A ALA* 3.0 30.9 + - - +
97A HIS* 3.1 25.3 + - - -
123A LEU* 3.9 1.3 - - - -
615C GLY 3.9 5.8 - - - -
616C GLY 5.3 0.7 + - - -
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Residues in contact with VAL 94 (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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92A GLN 3.4 1.8 + - - -
93A SER* 1.3 72.1 + - - +
95A LYS* 1.3 60.6 + - + +
97A HIS* 3.3 3.1 + - - +
98A PHE* 2.8 26.2 + - - +
120A ALA* 3.8 21.0 - - + +
123A LEU* 3.5 17.7 - - + -
124A ALA* 3.4 36.3 - - + +
127A GLN* 4.3 11.9 - - - +
129A LEU* 4.5 9.6 - - + -
131A PHE* 4.6 5.4 - - + -
135A ILE* 4.4 6.5 - - + -
615C GLY 4.4 3.4 + - - -
642C ILE* 4.3 22.9 - - + -
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Residues in contact with LYS 95 (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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64A THR* 4.2 8.1 - - + -
93A SER* 3.4 4.7 + - - +
94A VAL* 1.3 77.0 - - + +
96A ALA* 1.3 66.2 + - - +
98A PHE* 4.1 5.6 - - - -
99A PHE* 3.0 58.9 + - + -
131A PHE* 4.4 13.9 - - + -
618C PRO* 5.3 6.5 - - + +
641C THR 5.1 0.8 + - - -
642C ILE* 3.3 35.3 + - + +
644C GLU* 3.0 26.2 + - - +
646C ASP* 3.0 35.6 + - - +
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Residues in contact with ALA 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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64A THR* 3.7 18.9 - - + +
83A CYS* 4.0 9.8 - - - +
86A ALA* 4.0 11.4 - - + -
87A LEU* 3.8 24.2 - - + -
93A SER* 3.0 28.2 + - - +
95A LYS* 1.3 78.2 - - - +
97A HIS* 1.3 62.1 + - - +
100A LEU* 3.1 26.7 + - - +
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Residues in contact with HIS 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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87A LEU* 3.3 32.5 - - + +
91A GLY* 3.5 21.5 - - - -
93A SER 3.1 22.3 + - - +
94A VAL 3.7 2.9 - - - +
96A ALA* 1.3 78.8 - - - +
98A PHE* 1.3 61.8 + - - +
100A LEU* 3.7 3.3 - - - +
101A GLY 3.1 17.2 + - - -
116A ASN* 3.5 47.6 - - - +
119A ARG* 3.8 30.9 + - + +
120A ALA* 4.0 8.1 - - + +
123A LEU* 3.6 8.4 - - + +
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Residues in contact with PHE 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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94A VAL 2.8 22.0 + - - +
95A LYS* 3.9 7.4 - - - +
96A ALA 3.2 0.2 - - - -
97A HIS* 1.3 70.7 - - - +
99A PHE* 1.3 84.0 + + + +
101A GLY* 3.1 3.6 + - - -
102A GLN* 3.0 43.7 + - + +
117A LEU* 3.7 18.4 - - + +
120A ALA* 4.0 15.6 - - + +
134A ASP 4.3 4.3 - - - -
135A ILE* 4.1 24.7 - - + -
138A ALA* 3.6 31.6 - - + -
642C ILE* 3.7 39.3 - - + -
643C GLU* 4.4 2.5 - - + -
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Residues in contact with PHE 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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64A THR* 3.9 31.6 - - + -
65A ASN* 5.8 0.9 - - - -
67A ALA* 5.0 3.8 - - + -
68A LEU* 4.3 30.1 - - + -
71A LEU* 4.2 16.3 - - + +
83A CYS* 4.0 14.1 - - - -
95A LYS* 3.0 53.9 + - + +
98A PHE* 1.3 93.8 - + - +
100A LEU* 1.3 56.0 + - - +
102A GLN* 3.2 16.6 + - - +
103A CYS* 2.9 32.4 + - - -
642C ILE* 3.6 16.8 - - + -
643C GLU* 4.8 4.5 - - - -
644C GLU 4.7 1.6 - - - -
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Residues in contact with LEU 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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80A LEU* 3.5 35.9 - - + +
83A CYS* 3.6 23.7 - - + -
84A ARG* 5.3 2.2 - - + +
87A LEU* 4.1 20.2 - - + -
96A ALA 3.1 21.9 + - - +
97A HIS* 3.7 2.7 - - - +
99A PHE* 1.3 73.8 - - - +
101A GLY* 1.3 66.4 + - - +
103A CYS* 3.2 3.3 + - - +
104A GLN* 3.0 34.9 + - - +
116A ASN* 3.2 32.8 - - - +
644D GLU* 4.5 5.8 - - - +
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Residues in contact with GLY 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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97A HIS 3.1 12.0 + - - -
98A PHE 3.1 3.3 + - - -
100A LEU* 1.3 75.7 - - - +
102A GLN* 1.3 58.7 + - - +
104A GLN* 2.9 11.3 + - - +
105A LEU* 2.8 25.6 + - - +
113A ALA* 3.4 17.4 - - - +
116A ASN* 3.9 18.4 - - - +
117A LEU* 4.2 8.3 - - - -
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Residues in contact with GLN 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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71A LEU* 3.7 24.3 - - + +
98A PHE* 3.0 45.1 + - + +
99A PHE* 3.5 13.5 - - - +
100A LEU 3.2 0.2 - - - -
101A GLY* 1.3 77.3 - - - +
103A CYS* 1.3 60.8 + - - +
105A LEU* 3.5 12.7 + - + +
106A GLU* 3.2 27.7 + - - +
117A LEU* 4.5 7.4 - - + +
138A ALA* 5.0 5.3 - - + +
643C GLU* 2.9 29.1 + - - +
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Residues in contact with CYS 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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71A LEU* 3.7 19.3 - - - -
76A HIS* 3.9 14.9 - - - +
79A ALA* 3.5 35.2 - - - -
80A LEU* 3.9 22.2 - - + -
83A CYS* 5.0 1.3 - - - -
99A PHE 2.9 21.0 + - - +
100A LEU* 3.7 5.6 - - - +
102A GLN* 1.3 73.0 - - - +
104A GLN* 1.3 66.2 + - - +
106A GLU* 3.3 5.9 + - - +
107A MET* 3.1 28.8 + - - +
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Residues in contact with GLN 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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80A LEU* 4.3 12.8 - - + +
100A LEU* 3.0 29.3 + - - +
101A GLY 2.9 6.8 + - - +
103A CYS* 1.3 76.8 - - - +
105A LEU* 1.3 56.2 + - - +
107A MET* 3.1 5.8 + - - +
108A GLU 2.9 9.2 + - - -
109A SER* 2.8 41.0 + - - +
112A GLU* 3.1 12.8 - - + +
113A ALA* 3.0 27.4 + - + -
116A ASN* 2.6 34.5 + - - +
644D GLU* 3.5 18.6 + - - -
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Residues in contact with LEU 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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101A GLY 2.8 12.9 + - - +
102A GLN* 3.7 15.3 - - + +
103A CYS 3.3 0.2 - - - -
104A GLN* 1.3 76.8 - - - +
106A GLU* 1.3 60.7 + - + +
108A GLU* 3.2 19.4 + - - +
109A SER 4.9 0.7 - - - +
110A TYR* 4.0 25.9 - - + -
113A ALA* 3.8 11.3 - - + +
138A ALA 5.2 2.0 - - - +
141A ILE* 4.7 12.1 - - + -
142A ALA* 4.1 38.8 - - + +
145A LYS* 4.2 14.6 - - + +
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Residues in contact with GLU 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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71A LEU* 5.1 9.1 - - + +
74A GLN* 3.5 15.2 + - - -
76A HIS* 2.8 46.1 + - + +
102A GLN 3.2 16.6 + - - +
103A CYS* 3.3 4.7 + - - +
104A GLN 3.3 0.2 - - - -
105A LEU* 1.3 81.6 - - + +
107A MET* 1.3 60.6 + - - +
108A GLU* 3.3 10.7 - - - +
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Residues in contact with MET 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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76A HIS* 3.9 22.7 - - + +
77A GLU* 3.6 47.3 - - + +
80A LEU* 4.8 8.3 - - + -
103A CYS 3.1 18.3 + - - +
104A GLN* 3.1 7.1 + - - +
106A GLU* 1.3 79.0 - - - +
108A GLU* 1.3 64.9 + - - +
109A SER* 3.2 7.9 + - - +
38B VAL* 3.7 32.7 - - + +
39B GLY* 6.0 1.6 - - - -
40B ARG* 3.0 27.0 + - - -
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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