Contacts of the strand formed by residues 601 - 605 (chain A) in PDB entry 1GOG
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 601 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR* 3.9 10.0 - - - +
562A ILE 3.3 8.6 + - - -
563A SER* 4.3 6.6 + - - +
596A ASN* 3.7 2.9 - - - +
597A ASN* 2.8 44.2 + - - +
598A GLY 3.3 14.3 + - - -
599A GLY 3.2 2.9 - - - -
600A ASN* 1.3 79.3 - - - +
602A TYR* 1.3 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR* 3.2 4.0 - - - +
562A ILE* 2.6 55.7 + - + +
564A THR* 3.6 16.2 - - - -
567A SER* 3.3 14.0 - - - -
568A ILE* 2.9 61.6 + - + -
594A LEU* 4.1 24.7 - - + -
595A THR 3.1 15.9 - - - +
596A ASN* 3.9 26.4 + - + -
597A ASN* 3.7 3.6 - - - -
600A ASN* 3.6 21.1 + - - -
601A SER* 1.3 80.4 + - - +
603A SER* 1.3 62.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ARG* 5.6 5.2 - - - -
560A ILE 3.0 10.5 - - - -
561A THR* 3.0 21.3 + - - -
593A THR 3.8 0.2 - - - +
594A LEU* 3.4 5.1 - - - -
595A THR* 2.7 48.9 + - - -
597A ASN* 3.2 18.2 + - - -
602A TYR* 1.3 73.3 - - - +
604A PHE* 1.3 67.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A ARG* 3.4 6.2 - - - +
560A ILE* 3.0 74.4 + - + -
562A ILE* 4.2 20.0 - - + -
571A ALA* 5.6 0.2 - - + -
573A LEU* 5.1 6.3 - - + -
592A LEU* 3.9 31.6 - - + -
593A THR 3.3 23.1 - - - +
594A LEU* 3.9 18.8 - - + -
595A THR* 5.7 0.4 - - - -
603A SER* 1.3 80.5 - - - +
605A GLN* 1.3 70.6 - - - +
606A VAL* 4.3 7.9 - - + -
620A LEU* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A GLY* 2.6 37.3 + - - +
558A GLY 3.3 3.1 - - - +
559A ARG* 3.4 36.6 + - + +
592A LEU* 4.2 7.8 - - - +
593A THR 4.6 3.3 + - - -
604A PHE* 1.3 82.5 - - - +
606A VAL* 1.3 68.2 + - - +
607A PRO* 3.8 5.2 - - - +
608A SER* 5.2 5.2 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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