Contacts of the strand formed by residues 91 - 102 (chain A) in PDB entry 3MLQ
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PRO* 5.0 2.7 - - - +
77A PRO* 3.5 24.3 - - + +
89A THR* 3.4 33.7 + - + +
90A TYR* 1.3 77.0 - - - +
92A ALA* 1.3 58.9 + - - +
93A PRO* 4.3 1.2 - - - +
117A HIS* 3.1 47.3 + - + +
118A LEU 3.1 17.9 - - - +
119A PRO* 3.8 9.9 - - + +
120A LEU* 4.0 3.4 - - - +
95B TYR* 4.6 10.9 + - - -
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Residues in contact with ALA 92 (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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73A ILE* 3.5 13.8 - - + +
74A GLY 2.9 30.5 - - - +
75A ASP 4.4 6.5 - - - +
91A GLN* 1.3 74.3 - - - +
93A PRO* 1.4 65.3 - - + +
117A HIS* 4.5 2.2 - - - -
118A LEU* 2.8 34.7 + - + +
120A LEU* 4.1 23.2 - - + +
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Residues in contact with PRO 93 (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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72A ARG 3.7 0.7 - - - +
73A ILE* 3.5 3.3 - - - -
74A GLY* 2.6 53.4 + - - -
75A ASP 4.4 2.5 - - - +
77A PRO* 5.4 2.7 - - + -
91A GLN 4.5 2.2 - - - +
92A ALA* 1.4 86.0 - - + +
94A LEU* 1.3 58.1 + - - +
95A TYR* 4.2 8.3 - - + -
114A PHE* 4.0 14.4 - - + -
116A GLY 3.6 5.8 - - - +
117A HIS* 3.9 19.9 - - + +
77B PRO* 3.8 22.4 - - + -
78B PHE* 4.5 6.6 - - + -
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Residues in contact with LEU 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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44A ILE* 4.6 3.1 - - + -
48A PHE* 4.7 3.4 - - + -
71A TYR* 3.9 26.7 - - + -
72A ARG 3.5 14.1 - - - +
73A ILE* 3.9 15.0 - - + -
93A PRO* 1.3 73.3 - - - +
95A TYR* 1.3 67.4 - - - +
114A PHE* 3.8 2.6 - - - -
115A LEU* 2.8 46.7 + - + +
116A GLY 2.7 20.2 + - - +
118A LEU* 3.9 24.0 - - + -
344A PHE* 3.8 35.2 - - + -
382A LEU* 5.9 1.1 - - + -
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Residues in contact with TYR 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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71A TYR* 3.3 7.1 - - - +
72A ARG* 2.8 37.4 + - + +
93A PRO* 4.2 12.8 - - + -
94A LEU* 1.3 77.3 - - - +
96A ALA* 1.3 60.6 + - - +
112A GLU* 3.8 24.5 - - - +
113A VAL 3.4 7.4 - - - -
114A PHE* 3.5 50.6 - + + +
115A LEU* 4.6 2.7 - - - -
77B PRO* 6.2 0.7 - - + -
78B PHE* 3.6 33.7 - + - -
88B LEU* 3.9 16.6 - - + -
89B THR* 5.8 4.1 - - - -
91B GLN* 4.2 14.4 + - - -
117B HIS* 5.7 3.1 + - - -
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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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48A PHE* 4.3 11.7 - - + -
68A PHE* 5.0 1.6 - - + -
70A GLU 3.6 7.9 - - - +
71A TYR* 4.8 1.1 - - + -
95A TYR* 1.3 74.6 - - - +
97A ARG* 1.3 59.3 + - - +
98A LEU* 3.2 24.7 + - + +
112A GLU* 3.9 3.6 - - - -
113A VAL* 2.7 40.6 + - - +
115A LEU* 3.3 29.8 - - + +
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Residues in contact with ARG 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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69A LEU* 3.3 46.0 + - + +
70A GLU* 2.9 48.0 + - + +
71A TYR* 4.8 0.2 - - - +
96A ALA* 1.3 67.7 - - - +
98A LEU* 1.3 63.7 + - - +
110A GLU* 3.5 26.6 + - - +
111A ASP 3.4 7.6 - - - +
112A GLU* 3.3 33.4 + - + +
85B GLU 3.7 21.2 + - - -
86B LYS* 4.1 15.1 + - - +
87B ASP* 4.4 9.3 + - - +
360E LYS* 5.2 3.8 - - - +
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Residues in contact with LEU 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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52A PHE* 4.3 28.0 - - + -
66A LEU* 4.4 10.5 - - + -
67A ASP 3.8 12.1 - - - +
68A PHE* 4.3 12.1 - - + -
96A ALA* 3.2 25.3 + - + +
97A ARG* 1.3 80.0 - - - +
99A GLN* 1.3 62.1 + - - +
110A GLU* 3.4 4.5 - - - +
111A ASP 2.7 36.9 + - - +
113A VAL* 4.1 10.3 - - + -
115A LEU* 5.7 2.2 - - + -
351A LEU* 6.5 0.4 - - + -
369A PRO* 4.0 17.0 - - + -
373A VAL* 3.4 34.8 - - + -
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Residues in contact with GLN 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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65A VAL 3.6 1.7 - - - +
66A LEU* 3.3 8.9 - - - +
67A ASP* 3.1 46.7 + - - +
69A LEU* 3.7 32.6 - - + +
98A LEU* 1.3 79.2 - - - +
100A LEU* 1.3 57.1 + - - +
101A ILE* 4.4 16.0 - - + +
108A ILE* 3.4 28.2 - - + +
109A LYS 3.2 6.3 - - - -
110A GLU* 4.5 3.1 - - + -
369A PRO* 4.1 1.4 - - - +
341E ARG* 2.8 30.9 + - - -
343E VAL* 4.6 9.1 - - - +
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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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64A LEU* 3.3 42.4 - - + -
65A VAL 3.7 7.4 - - - +
66A LEU* 4.0 16.8 - - + -
99A GLN* 1.3 71.8 - - - +
101A ILE* 1.3 63.6 + - - +
102A HIS* 3.7 13.0 + - + -
107A LEU 3.4 2.8 - - - +
108A ILE* 3.4 4.6 - - - -
109A LYS* 2.8 33.6 + - + +
359A MET* 4.4 1.1 - - + -
367A LEU* 3.5 35.2 - - + +
368A THR* 3.8 5.8 - - - +
369A PRO* 3.7 15.7 - - + +
372A LEU* 4.0 17.3 - - + -
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Residues in contact with ILE 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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64A LEU* 3.5 8.2 - - - -
65A VAL* 2.8 55.1 + - + +
67A ASP* 5.5 5.4 - - + -
99A GLN* 4.4 18.4 - - + +
100A LEU* 1.3 72.9 - - - +
102A HIS* 1.3 72.9 + - - +
103A LYS* 3.5 6.3 + - + +
106A GLY 4.9 0.7 - - - +
107A LEU 3.6 2.7 - - - -
108A ILE* 3.6 20.0 - - + -
343E VAL* 4.0 25.1 - - + -
344E LEU* 3.9 35.9 - - + +
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Residues in contact with HIS 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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63A GLY 4.4 0.2 - - - -
64A LEU* 3.1 27.3 - - + +
100A LEU* 4.2 22.5 + - + +
101A ILE* 1.3 70.8 - - - +
103A LYS* 1.3 55.8 + - - +
104A ASP* 4.2 6.3 - - + +
105A THR* 4.2 12.3 - - - +
106A GLY* 2.5 37.9 + - - -
107A LEU* 2.9 48.4 + - + +
109A LYS* 5.4 5.2 - - + -
364A PRO* 3.1 32.0 + - + -
365A ASP* 4.5 10.0 - - - -
367A LEU 4.4 5.8 + - - -
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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