Contacts of the strand formed by residues 798 - 804 (chain I) in PDB entry 6ALG
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 798 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692I THR* 3.8 7.9 + - + +
694I ARG* 2.8 36.5 + - - +
696I ASP* 3.8 18.9 - - + +
797I GLY* 1.3 79.1 - - - +
799I ASN* 1.3 61.4 + - - +
800I MET* 3.5 11.8 - - + +
827I ARG* 2.7 73.5 + - - +
828I PHE* 4.6 9.6 - - + -
1231I TYR* 3.9 4.3 - - - -
1232I MET 2.8 29.1 + - - +
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Residues in contact with ASN 799 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696I ASP* 3.4 21.1 + - - +
697I LYS* 2.8 28.5 + - - +
698I PRO* 4.1 0.4 - - - +
699I LEU* 3.3 42.4 - - + +
798I GLN* 1.3 73.0 - - - +
800I MET* 1.3 66.3 + - - +
827I ARG* 3.7 10.2 + - - -
1229I TYR* 4.5 11.3 - - + -
1230I MET 3.3 12.3 - - - +
1231I TYR* 3.7 16.2 - - + +
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Residues in contact with MET 800 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798I GLN* 3.5 23.3 - - - +
799I ASN* 1.3 78.4 - - - +
801I ARG* 1.3 65.1 + - - +
802I VAL* 3.4 3.1 + - - +
822I VAL* 3.9 19.3 - - + -
827I ARG* 4.3 18.6 - - - +
828I PHE* 3.5 35.9 - - + -
1095I ASP* 4.1 17.0 - - + +
1096I ILE* 3.6 27.4 - - + -
1229I TYR* 3.2 10.0 - - - +
1230I MET 3.0 31.7 + - - +
1232I MET* 3.8 14.8 - - + -
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Residues in contact with ARG 801 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800I MET* 1.3 72.2 - - - +
802I VAL* 1.3 62.1 + - - +
1088I ASP* 3.0 30.1 + - - +
1092I THR* 3.7 19.0 + - - -
1093I PRO 3.7 19.1 + - - -
1094I VAL* 3.3 16.3 - - + +
1095I ASP* 2.8 42.9 + - - +
1096I ILE* 2.9 10.2 + - - +
1119I MET* 3.9 25.4 - - - +
1122I LYS* 5.7 1.2 - - - +
1210I ILE* 4.5 0.8 - - - +
1227I VAL* 4.2 22.1 - - + +
1228I GLY 3.4 8.5 - - - +
1229I TYR* 3.5 38.7 + - + +
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Residues in contact with VAL 802 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800I MET 4.1 3.1 - - - +
801I ARG* 1.3 74.6 - - - +
803I ALA* 1.3 71.8 + - - +
804I PHE* 4.1 11.0 - - + -
1094I VAL* 3.6 2.0 - - - -
1096I ILE* 3.0 15.0 - - + +
1098I LEU* 3.7 24.7 - - + -
1115I THR* 3.8 17.8 - - + +
1227I VAL* 3.1 6.6 - - - +
1228I GLY 2.8 40.9 + - - +
1230I MET* 3.7 33.9 - - + +
1232I MET* 5.4 2.9 - - - -
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Residues in contact with ALA 803 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802I VAL* 1.3 74.3 - - - +
804I PHE* 1.3 67.6 + - - +
805I MET* 3.8 12.6 - - + -
1094I VAL* 3.4 25.5 - - + +
1096I ILE 2.9 6.5 + - - -
1097I VAL* 3.5 10.7 - - + -
1098I LEU 2.9 26.2 + - - -
1212I LEU* 4.6 6.5 - - + -
1225I VAL* 4.9 1.3 - - + -
1226I THR 3.3 9.9 - - - +
1227I VAL* 4.0 9.0 - - + -
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Residues in contact with PHE 804 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802I VAL* 4.1 9.9 - - + -
803I ALA* 1.3 80.0 - - - +
805I MET* 1.3 61.6 + - - +
1098I LEU* 3.6 36.8 - - + -
1099I ASN 4.9 6.3 - - - -
1100I PRO* 3.5 15.5 - - + -
1103I VAL* 5.4 2.5 - - + -
1111I GLN* 4.6 13.2 - - - -
1112I ILE* 4.1 17.7 - - + -
1115I THR* 3.8 20.6 - - + -
1225I VAL* 4.2 2.7 - - - +
1226I THR* 3.0 28.6 + - + +
1230I MET* 3.8 23.8 - - + -
638J SER* 3.3 35.5 - - - +
639J VAL* 4.4 15.5 - - + +
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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