Contacts of the strand formed by residues 107 - 115 (chain A) in PDB entry 3LW6
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 4.3 13.8 - - + +
75A HIS 3.8 18.3 + - - +
76A LYS* 3.5 17.6 - - + -
77A MET 3.0 19.4 + - - -
105A GLY 3.5 4.9 + - - +
106A VAL* 1.3 74.5 - - - +
108A HIS* 1.3 64.2 + - - +
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Residues in contact with HIS 108 (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 MET* 3.0 33.7 - - + +
79A LEU* 4.3 2.9 - - + -
98A THR* 4.3 29.7 + - + +
101A LEU* 3.7 36.7 - - + +
102A LYS* 5.1 9.0 - - + -
106A VAL* 3.0 20.9 + - + +
107A ALA* 1.3 75.5 - - - +
109A HIS* 1.3 74.8 + - - +
110A ILE* 4.3 14.5 - - + +
138A TYR* 4.4 6.3 - - - -
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Residues in contact with HIS 109 (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 MET 3.1 4.0 + - - -
79A LEU* 2.9 25.2 + - - -
108A HIS* 1.3 81.8 + - - +
110A ILE* 1.3 77.8 + - - +
111A PHE* 3.5 26.2 - + + -
138A TYR* 3.2 27.5 - - + +
290A PRO* 3.5 42.5 + - + +
291A VAL* 4.1 2.5 - - - -
292A THR* 2.8 31.5 + - - -
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Residues in contact with ILE 110 (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* 3.7 24.5 - - + -
81A VAL* 4.0 22.2 - - + -
90A LEU* 5.1 0.2 - - + -
93A PHE* 4.1 19.1 - - + -
94A VAL* 4.2 20.9 - - + +
97A MET* 4.7 4.0 - - + -
98A THR* 4.2 13.9 - - - +
108A HIS* 4.3 9.2 - - + +
109A HIS* 1.3 82.6 + - - +
111A PHE* 1.3 62.3 + - - +
112A VAL* 4.1 8.7 - - + -
289A VAL* 5.2 1.6 - - + -
290A PRO 4.9 1.8 + - - +
291A VAL* 3.7 34.2 - - + -
292A THR 3.0 25.3 + - - +
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Residues in contact with PHE 111 (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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78A ALA* 3.8 24.2 - - + -
79A LEU 2.9 14.2 + - - +
80A LEU* 4.0 15.0 - - + -
81A VAL* 2.9 27.7 + - - +
109A HIS* 3.5 42.6 - + + -
110A ILE* 1.3 71.9 - - - +
112A VAL* 1.3 63.8 + - - +
113A LEU* 3.6 12.3 + - + +
130A GLY 5.6 0.9 - - - -
133A PHE* 3.9 32.3 - + - -
134A ALA* 4.1 10.1 - - + -
135A SER 5.1 0.4 - - - -
138A TYR* 3.8 21.3 - + - -
292A THR* 3.4 24.2 - - + +
294A LEU* 4.8 5.6 - - + -
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Residues in contact with VAL 112 (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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81A VAL* 3.7 6.5 - - + +
83A PHE* 3.5 42.6 - - + -
90A LEU* 3.8 23.1 - - + -
110A ILE* 4.1 5.6 - - + -
111A PHE* 1.3 71.3 - - - +
113A LEU* 1.3 62.1 + - - +
114A ASN 3.4 2.4 + - - +
291A VAL* 3.6 27.8 - - + -
292A THR 2.8 8.3 + - - -
293A ILE* 3.5 27.5 - - + +
294A LEU* 2.8 31.2 + - - +
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Residues in contact with LEU 113 (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* 4.0 19.7 - - + -
81A VAL 2.8 21.1 + - - +
82A PRO 4.4 0.2 - - - -
83A PHE* 3.0 22.7 + - - +
111A PHE* 3.7 20.2 - - + +
112A VAL* 1.3 72.0 - - - +
114A ASN* 1.3 61.6 + - - +
115A GLN 3.4 1.2 + - - -
126A LEU* 3.2 40.6 - - + +
127A ILE* 3.9 15.3 - - + +
130A GLY* 3.7 23.3 - - - -
294A LEU* 3.8 20.4 - - + -
296A ILE* 3.8 19.5 - - + -
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Residues in contact with ASN 114 (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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83A PHE* 3.2 34.7 - - + +
84A ARG* 4.2 4.9 - - - +
85A ASP 5.0 0.5 + - - -
112A VAL* 3.4 1.1 + - + +
113A LEU* 1.3 69.7 - - - +
115A GLN* 1.3 67.3 + - - +
116A VAL* 3.2 15.1 + - - +
293A ILE* 4.0 14.3 - - + +
294A LEU 2.8 17.7 + - - +
295A ASN* 2.9 24.7 + - - +
296A ILE* 2.8 29.8 + - - -
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Residues in contact with GLN 115 (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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83A PHE 2.9 13.3 + - - +
84A ARG* 3.3 42.1 + - - +
113A LEU 3.4 1.6 + - - -
114A ASN* 1.3 71.8 + - - +
116A VAL* 1.3 60.4 + - - +
117A ASP* 2.8 40.1 + - - +
119A PHE 4.0 0.2 - - - -
120A ARG 3.0 22.8 + - - -
121A PHE* 3.4 9.5 - - + -
122A ASN 2.9 23.4 + - - -
126A LEU* 3.6 21.5 - - + +
205A TRP* 4.0 2.4 - - - -
296A ILE 3.6 4.3 - - - +
298A LEU* 3.8 19.6 - - + +
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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